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It may remain a mystery. I agree with you, the eye coloring and shape doesn't make me think Marek's, it's more like Coloboma that I have seen in photos and threads here on BYC. AND he's had an issue with his eye since hatch, so defect would "fit" better. He's a cute fella!

If you are able to get testing, let me know what you find out. It's curious that the issue has been since hatch. MG can be transmitted vertically to the embryo, but my thoughts is the chick would have developed more symptoms or failed to thrive, but who knows...could be just a very mild...

Does your vet college offer services? I wonder if you could persuade a professor to help you run a culture to see if you can figure out if the cause is bacterial, fungal, etc. and what would be the most effective treatment to use. Wonderful that you are going to school to learn all of this...

Poor thing, the bubbles are still there:( If you have a vet that can run testing that's always best. Hard to know the cause of the chronic irritation since it's been there since hatch. Possible she may have Mycoplasma. You can try giving an oral antibiotic like Tylan/Tylosin to see if that...

Try again with the rinsing then applying your ointment 2X a day, work on it really well for a while. If it does not clear up, then consider giving her a round of Tylan/Tylosin to see if that makes a difference, but it's best to see if this will clear up without antibiotics.

The bubbles look a bit odd, when you can get a few more photos of that eye with the bubbles. When you clean the eye, do you ever get any pus?

Try flushing the eye with saline and remove as much debris from the eye as possible. Then apply your ointment in the eye. Do this a couple of times a day.