Well, this got interesting. Cheers to both of you, the various explanations make enough sense and/or are sufficiently plausible for my (extremely lax) standards that I'm not really fussed by it anymore.
Quote Originally Posted by GoktimusPrime View Post
The nature of their upgrades may have differed due to Optimus Primal's transformation having been somehow influenced or affected by the Matrix; if in no other sense, cosmetically (i.e. no organic appearance). Although having a fourth mode, deployable shields, gatling cannons etc. is pretty significant (it doesn't make Primal unbeatable of course, but it's certainly impressive nonetheless).
Just tossing this out there, but if you include Prime's trailer (and/or Roller) he sorta does have multiple alt-modes. It's a bit of a stretch, but no more so than a lot of TF lore let alone fanon.
Or you could just, you know, use the actual reason, but that's far less fun.