Honestly, I would be very surprised if he were disallowed. Not only because, as you said, it is unclear if the 12th amendment eligibility conditions apply to conditions added after the 12th amendment and make no reference to modifying it. But also because the 22nd amendment does not, in fact, specify that someone who has served two terms is ineligible to be President. Rather it is very specifically a condition about being elected to president. If we’re interpreting the constitution strictly literally, the 22nd amendment doesn’t make a new condition for eligibility to be President, only for being elected president. So the 12th amendment would not apply. That may not have been the intent, but if anyone thinks the same Supreme Court that ruled that the President has absolute immunity on the use of his presidential powers isn’t going to let Trump slide right through that loophole… well, you could probably convince them it was raining as you piss on their leg.