I believe the answer is that it's undoubtedly non-factual. The linked text confuses the terms the manuscript tries to discuss. I am positive that the Bhagavata passage is a reiteration of a much older concept.
I will address the claims in the text mentioned by this question one by one.
Bhagavata Purana is not 5100 years old. There is some dispute but it is generally understood that it was written between the 8th and 10th century AD, or as early as the 6th century at maximum.
A photon is not made up of six particles; it's indivisible. It's definitely not made up of six atoms, as that would make it a molecule.
Concerning this passage:
Translation : Division of gross time is calculated as follows: Two
atoms make one double atom, three double atoms make one Hexatom. This
Hexatom is visible in the sun light which enters through the holes of
a window screen. One can clearly see that the Hexatom goes up towards
the sky.
There is no such term in modern physics as a "hexatom", interpreting it liberally let's assume it's talking about a group of six atoms. I'm not sure if the original manuscript can be translated this way, so maybe the transcription itself is inaccurate.
I don't see anything that would suggest that this is a description of a photon. This text suggests a progression from a fundamental unit (aṇuḥ), which is invisible, up to "trasareṇuḥ" which is the smallest particle visible to the naked eye.
It mentions that the "hexatom" or "trasareṇuḥ" is visible in the sun light, so it's something separate from the light. This sounds like a description of a speck of dust floating in the air, being illuminated by the sunlight through a hole. Certainly if it was a quantum scale object it would not be visible to the naked eye.
According to the full text in context, trasareṇuḥ is simply a unit of measurement that appears in a progression of units in a system of belief similar to atomism. Atomism was proposed in the 5th century BC by the Greek philosopher Leucippus. Based on these facts, we can confidently conclude that this passage from Bhagavata is a reiteration of this idea. The idea that the world is made up of small indivisible particles invisible to the naked eye was around for hundreds of years by the time it was written.
