I understand your reservations, but it might be misguided to expect it to "look transparent". 5th Gen EOTS are "hanging" from the chin so to speak, so viewed from the side you can more or less see through the EOTS module.
The one on J-36's chine cannot be see through from the side, being embedded the side aspect will be "blocked in".
It will only be see through from the top-down aspect. Coatings might be applied to make it less transparent.
Speaking of alternatives, I saw a post by foolsball comparing the apertures to a snakes "infrared vision". 2 partially overlapping infrared sensors could be used to overcome the depth/vector shortcomings of a single IRST setup.