Two newly published articles reveal the significance of Akbar the Great and the continuing relevance of his ideas:

http://thewire.in/2015/10/12/recalling-the-lessons-of-kabir-and-akbar-for-these-turbulent-times-12973/

http://scroll.in/article/761493/how-the-mughals-used-sanskrit-to-become-the-rulers-of-india

From the scroll article (link given in the original post (OP) of this thread):

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The Mughals also turned to Sanskrit intellectuals for information concerning other Indian practices and ideas that could inform an imperial agenda, including the notion that Akbar was an incarnation of the Hindu god Vishnu. Bada’uni unhappily attests that Brahmans introduced Sanskrit works that predicted Akbar’s rise to power as Vishnu’s avatar:

[Cheating imposter Brahmans] told [the king] repeatedly that he had descended to earth, like Ram, Krishan, and other infidel rulers, who, although lords of the world, had taken on human form to act on earth. For the sake of flattery, they presented Sanskrit poetry [shi‘r-ha-yi hindi] allegedly uttered by tongues of sages that predicted a world-conquering padshah would arise in India. He would honor Brahmans, protect cows, and justly rule the earth. They wrote such nonsense on old papers and presented it to [the emperor]. He believed every word.

Some Sanskrit works written under Akbar’s support mirror these claims rather precisely. For example, in his bilingual grammar from the late sixteenth century, Krishnadasa praises Akbar as Vishnu embodied:

Since Brahma was described by the Veda

as changeless and beyond this world,

therefore Akbar, great ruler of the earth, was born

in order to protect cows and Brahmans.

His virtuous name is celebrated throughout the ocean of shastras

and among scriptures [smriti], histories [itihasa], and the like.

It is established forever in the three worlds, and

therefore with his name this work is composed.

It is no surprise that cows were protected by Lord Krishna, son of Gopala,

and the best of the twice born guarded

by the Ramas, gods of the Brahmans.

But it is truly amazing that the lord Vishnu

descended [avatirna] in a family of

foreigners that loves to harm cows and Brahmans.

Akbar protects cows and Brahmans!

Jains also provided Akbar access to certain Sanskrit-based practices that would prove politically potent, such as sun veneration. Bhanucandra, a Tapa Gaccha ascetic whom Hiravijaya sent to the Mughal court in Lahore in 1587, taught Akbar how to recite a Sanskrit text titledSuryasahasranama (Thousand Names of the Sun). Siddhicandra, Bhanucandra’s Sanskrit biographer, tells the tale thus:

One time, the ruler of the earth repeatedly asked the Brahmans for the Thousand Names of the Sun, but they could not find it anywhere. By a stroke of luck they located some wise man. He gave [the text] to them, and they presented it to the glorious shah [shrisaha]. Having seen it, the glorious shah said to them excitedly, “Tell me who among good people can teach me this?” They replied, “Only one who has subdued all the senses, sleeps on the ground, and possesses sacred knowledge is qualified in this matter.” When he heard this, the shah said, “Only you [Bhanucandra] possess such qualities here. You alone, venerable one, will teach me this every morning.”

Later in his work, Siddhicandra portrays Akbar as devoted to honouring the sun to the exclusion of other religious activities:

The glorious shah diligently learned the Thousand Names of the Sun.

He forgot any other taste and recited the names there. He devoted his

mind, stood in the correct direction facing the sun, and learned from

Bhanucandra with his folded hands pressed against his forehead.

Siddhicandra does not explain further this “other taste” (anyarasa) for which sun veneration eliminated any need on the part of the Mughal emperor. But it is likely a covert reference to Islam, especially given that Siddhicandra carefully mentions that Akbar faced the correct direction in venerating the sun and used his head and hands properly, which are both important concerns in Islamic prayer as well. Furthermore, Bada’uni, a notorious critic of Akbar in his unofficial history of the era, testifies that this ritual occurred up to four times daily, including at times for Islamic prayers such as sunrise. Jerome Xavier, a European traveler, even noted Akbar’s predilection for sun worship as one reason why he was best not considered a Muslim. Most likely, rather than indicating his personal religious inclinations, Akbar designed this royal custom to promote his absolute sovereignty.

From The Wire article (link given in the OP):

Jalaluddin Muhammad Akbar, who ruled most of India for almost half a century between 1556 and 1605 was totally illiterate. But he had the innate inquisitiveness to question virtually everything and only a convincing reason would satisfy him. He questioned the use of several letters for the same sound in the Arabic alphabet, the inhumanity of child marriage, the denial of a daughter’s share in her father’s property, the treatment of sexuality as mere pious duty rather than a source of pleasure, but above all, he questioned denominational religion as the basis of legitimacy of the state.

Indeed, he firmly held that “truth inhabited every religion; how was it then that the Muslim community, which was relatively young, less than a millennium old, should receive preference at the expense of others?” The notion of any religion-based state would necessarily involve discrimination against other religionists. To seek a resolution between his quest of a common truth and religious discrimination, Akbar established the famous Ibadat Khana (House of Worship) where first the Ulama (Islamic theologians) and soon others – Brahmins, Jesuits, Jains, Zoroastrians – discussed the truth of their respective religions. In the end, Akbar arrived at the concept of sulh-i kul, universal peace, which would be entirely non-discriminatory.

It was Akbar’s courtier, historian and counsel, Abu’l Fazl, author of Akbar Nama, who created the conceptual architecture of sulh-i kul. Clearly this was a total alternative to the concept of a religion-based state. Abu’l Fazl elaborates the qualities that mark out a great monarch. Lineage, collection of wealth, and the assembling of a mob are not essential for this rare dignity, in Abu’l Fazl’s words; “on coming to the throne, if the king did not establish sulh-i kul for all time and did not regard all groups of humanity and all religious sects with the single eye of favour and benevolence and not be the mother to some and step-mother to others, he will not become worthy of the exalted dignity.”

Already in the Islamic world, huge, stimulating debates were taking place on various facets of religion; many Sufi ideologues were enlarging the space that a dogmatic view of Islam had created. Mansur al-Hajjaj challenged it with his immortal assertion ‘an al-Haqq’ (‘I am the Truth, or I am God’) meaning Truth or God resides in each one of us and no one has a monopoly of it. Ibn al-Arabi postulated the notion of the unity of Being (wahdat al-wujud), which opened the way to pantheistic or multiple paths of approaching God instead of a hidebound one laid down by the theologians. At times even the authenticity of the Quran as divine revelation was questioned. There were also heated debates on the relation between reason and faith among intellectuals.

Back home in Akbar’s court, Faizi the poet, Abu’l Fazl’s elder brother, had expressed doubts about Islam’s claims to the finality of truth: “Wherefore diversity of practice in Islam? Wherefore allegories in the words of the Quran? If such be the truth of Islam in this world, kufr can have a thousand smiles”, he iterates in a poem. Abu’l Fazl was well up to date in these debates. His own intellectual evolution moved through several highways and by-lanes and their influence on him is evident.