None of the rexes have a single model change. SOmeone with a 3D model viewer confirmed this with BestInSlot and together, shared some images on a video Conor made. over a week a ago.
And I don't think the names are mismatched, I think one, they're just in the order you weren't expecting. Also, the skin colors are based on how they clearly looked in the films, rather than from behind the scenes, as I can show an example here with the female from the end of the Lost World film.
The female is the one to the right side. Her brown colors and patterns were shown on the animatronics used for her, but those colors, while present at some points on-screen like when she and the male first arrived at the trailer, was too dark (and at one point, blurry, when the heroes were bringing the child rex outside).
(A similar thing happened with the Triceratops and the Parasurolophus.)
Based on my observations, I think the decision was to visually portray the dinosaurs (excluding the Lost World pteranodon in regards to the model shapes and lack of teeth) the best can as they did on-screen with enough clearance for reference, rather than from behind the scenes. When I think about it more deeply, it makes sense, because people from the general public are going to remember how they looked on-screen rather than what they "really looked like" from behind the scenes, as the only ones who will know of the latter would be fans, like myself and probably you as well, who go deeper into the series than the general audience.
The 2001 rex colors I don't think were added because they were too similar to the green rex (which was used for the male, more clearly similar to when he and the female were shown at the trailer when searching for their infant than his CGI model like above). Even looking at the green 1997 rex can be easily related to the green rex from JPIII. The raptors I believe got the same treatment, particularly the 1997 versions. The female raptors weren't orange on-screen, but they were given a more duller version of the male for both naming consistencies and to be able to distinguish it from the 1993 version, as the 1993 raptor designs were reused on-screen.
The Stegosaurus and the Triceratops don't have legacy skins for the 2001 or 1997 respectively because they are basically the same designs as they were in their previous films.
