It's been a while since I watched GT for the last time, so the in-depth story details about Gohan is something I won't remember so well. But since some here also used the visual as an indicator, I think I can give my shot on that.
It's very inconsistent, and there's enough evidence to support both sides (Permanent Ultimate / Non-Permanent Ultimate), it depends on the moment, the story we're set in.
The Old Era ended shortly after Gohan got his upgrade so we couldn't see much from Toriyama except the EoZ, which suggested that the Ultimate was permanent for his “base form”, and the anime followed that concept, we never see Gohan's original “Goku style” eye design returning after that.
But when it comes to the animations, it is no different from the Revival / Modern era. Toei apparently intended to follow something similar to what is seen in Super, but they kept switching between concepts and designs, and Toriyama did that as well when he returned to the franchise.
- The Tapion Movie has Gohan keeping the
original base form design, and then transforming into
Ultimate.
- Toriyama's designs for GT featured Gohan with his
eye design looking accurate to the way it looked in the EoZ. But Toei apparently interpreted that as his base form, as he keeps that
design throughout the entire series, and also transforms into a SSJ.
- In “Son Goku & Friends Return” we don't see Gohan fighting nor transforming. In the manga, he has the
regular base form eye design.
- In the OVA, it's the
Ultimate eye design. Though you can also find the original eye shape in the
character model sheets, or even the
full original base form design.
- For Battle of Gods, Toriyama drew Gohan with glasses but with his base form eye design in his
classic illustration. But he also drew the character design references with
Gohan having the eyes looking just like the way they did in EoZ.
- In the trailer for the movie, it's just like how it was seen in GT,
the base form has the Ultimate eye design, but he transforms into a SSJ.
- The final movie though, suggests the Ultimate is permanent, and that he only needed the SSJ for the ritual.
The Ultimate adds a bang in front of his forehead.
- The Beerus arc in Super, both the
Manga and
Anime, seems to follow that same concept, permanent Ultimate, with the exception that it doesn't add the bang.
- That continues in the manga until the
Moro arc.
- In Fukkatsu no ‘F’ and Golden Freeza arc, the GT concept returns, but for the first time, Gohan has his original base form eye design again while wearing the glasses. This applies to all versions of the arc. (
Movie /
Anime /
Manga)
- In the Super anime, that concept is kept, but his
Ultimate eye design returns for his base form again, that is in the fillers right after the Zamasu arc, and
continues into the ToP arc. Ultimate gives him the bang.
- Super Hero in both the
movie and
manga continues the concept established in Fukkatsu no ‘F’. Base form with original eye design > SSJ > Ultimate.
- Daima has the
Ultimate design, but we don't know if he's transformed, if it's permanent Ultimate, or if it's meant to be his base form. Given how it's a shot with everyone in their regular appearances, it might be one of the latter two.
You can even say that there's a 4th interpretation there, which would be the “Ultimate SSJ” interpretation, I think there's evidence for that too, but I believe it would apply to GT only, as Super seems pretty consistent to me in regards to Gohan not being able to use the SSJ after he transforms into Ultimate.
As for the initial post theory, I like it. But I think you can also view Gohan unlocking his ultimate power as a supernatural ability he got after the Ro Kaioshin ritual. It's not something that is related to his DNA or cells like the SSJ does, it's something “external” that only he has access to and not training to keep it made him lose it. Baby being the artificial entity he is, had his physical limitations, so would not be able to access the Ultimate power boost. What he got access to at best were SSJ and Oozaru transformations, which are part of Saiyajin DNA. Natural inner power ups.
It's similar to Cell, he had the cells from a Goku who had the Kaioken and Genkidama, but he couldn't use any of the two because those are highly advanced supernatural techniques that demand the Kaio training for them to work, that's why no one is able to replicate them only by observing Goku. (I know Cell says he can do the Genkidama, but we never saw it, so I believe he was just joking, like how we see other many characters saying that they're able to do this and that but we never actually see them doing it. I believe he needed the training at least, or Goku touching him with such techniques, just like he did with the Shunkan Ido)
Toriyama's Power Level: Infinite. Above All Characters, literally the creator and ultimate mind behind the DB's realities [R.I.P]