I figured out how to have changed tissue layers!
Use a tissue layer that is completely unrelated to the original, such as foot fat, and completely remove any related modifiers from the original creature.
Yes, it's hackish. Yes, it's ugly. Yes, BOTH have to be done.
For example, say you have a creature with black, curly, greasy hair and you want to make it blonde. First, remove the black hair from the creature entirely. It's required. Second, make the unrelated tissue have the gold color modifier and use [TLCM_NOUN:hair:SINGULAR] to make it appears as "his hair is gold."
It's pretty freaking horrible, I have to admit.
I think you could make a new standard tissue setup for creatures only used for transformations. Something like this:
Then you could assign the appropriate tissues to the new creature's tissue layers (like BODY_HAIR_TISSUE_LAYERS:T_HAIR, or for VERTEBRATE_TISSUE_LAYERS you send in T_SKIN, FAT, MUSCLE, BONE and CARTILAGE, etc.) Coloring the T_tissue would have no reason to crash the game, I think, and everything would be copacetic. If vanilla transformations are like having one's tissues twisted around to form some kind of metamorphosis, a separate tissue setup means one's tissues themselves twist and mutate into novel forms, and it is this molecular shifting that results in the shape of some other kind of creature.
Besides, it doesn't even work most of the time, it seems. So I guess it can be ignored. But hey, I'm looking for more ways.
Edit 6: Do creatures just refuse to transform after their first time in fort mode? If so, I'm going to have to make that Super Saiyan transformation last the entire time until they get access to Super Saiyan 2...
IIRC, only one creature transformation can be in effect at any given time. It throws a wrench in Polymorph Control to be sure.
For your Super Saiyans, have you considered an OVER layer, gas-state 'energy' tissue to cover their bodies? You could specially color the eye energy tissue of the Supers teal or something, the hair's golden yellow, and maybe call the upper body's energy tissue 'aura'. Just replace the usual app modifiers to select the new tissues and it should look something like "His eyes are teal. His hair is golden yellow. His aura is gold."
The energy material (since DBZ already laughs at physics) could be absurdly dense, making them even stronger, but it would need an extremely fast healing rate to make up for the "right foot aura is gone" type messages. Over-layer tissues could work for Oozaru eyes and hair as well.
Just my untested thoughts.