Here is a compressed order of events in the Gen 1 continuity:
- Orion Pax is heavily damaged/killed
- Alpha Trion rebuilds Orion Pax into Optimus Prime, presumably giving him the Autobot Matrix of Leadership. It could be argued that the Matrix was partly responsible for the upgrade, but this is never stated one way or another.
- Optimus Prime is heavily damaged, and in his last moments, gives the Matrix of Leadership to Ultra Magnus. No change is made to Optimus Prime
- Ultra Magnus inserts the Matrix into his own chest, but receives no upgrade.
- Ultra Magnus is temporarily destroyed, and the Matrix goes to Hot Rod who wears it as bling.
- The Matrix activates during the Autobot's "Darkest Hour™" and Hot Rod is upgraded into Rodimus Prime.
- In three instances in Season 3, Rodimus removes the Matrix and instantly reverts back to Hot Rod. When he reinserts the Matrix after the first two removals, he is instantly transformed back into Rodimus Prime. The third removal is permanent, and he remains as Hot Rod from then on.
- Galvatron inserts the Matrix into his canon and only gets visions of Autobots. He recieves no reformatting/upgrade like Hot Rod. This could be hand-waved away arguing that the Matrix only works on Autobots.
- Scourge inserts the Matrix into himself and has his power levels increased, but goes a bit insane. He receives no reformatting/upgrade like Hot Rod. This could be hand-waved away arguing that the Matrix only works on Autobots.
- Optimus is revived twice (once as a sort of Zombie-Prime). In both cases, when he reinserts the Matrix, he receives no new reformatting/upgrade.
- In Beast Wars, Optimus Primal merges his spark with that of Gen 1 Optimus Prime. When he does so, he is upgraded into Optimal Optimus. When The sparks are split again, he reverts back to Optimus Primal. Only Sparks are mentioned here, with no mention of the Matrix being specifically transferred.
So, after all that...
Why is Hot Rod the only one that is magically reformatted when he inserts/removes the Autobot Matrix of Leadership?