From here.
Optimus Primal is frequently called and referred to as "Supreme Commander" or "Commander" in the Japanese dub of the Canadian series. "Supreme Commander" is the equivalent of calling him "Optimus."
Not... quite. Optimus Primal has always been commander, but he was initially the commander of the Axalon on an expeditionary mission, not a military one. And he also had dealings with the Maximal Council (re: Protoform X), so he was obviously a Maximal of higher ranking. The real shift in Beast Wars was from being a civilian commander to a military one. Also, in the Japanese dub of the Canadian series, Convoy was always called "Supreme Commander or just "Commander."
ONLY when he combines the power of his Energon Matrix with that of Lio Convoy's. Optimus Primal would be unable to do this in the Canadian series as he is never in the company of another Matrix-bearing Maximal.
We never saw the inside of Season 1 Optimus Primal's chest. I'm not saying that Larry DiTillio or Bob Forward ever intended for Optimus Primal to have a Matrix in his chest, but the presence of one in the BWII movie does not contradict the Canadian series. There's a greater contradiction in G1 where:
* in the comics the Creation Matrix was initially an intangible artifact in Optimus Prime's head which he could even transfer into a human's mind. It was later portrayed as a physical artifact in Optimus Prime's chest, like in TFTM, which also proved problematic as it meant that the Autobots had inadvertantly disposed of the Creation Matrix when they buried his original body in space (hence the Matrix Quest and the retconned excuse that the existence of the physical Matrix was a secret).
* in the G1 cartoon we saw the inside of Optimus Prime's chest which housed his Cosmitron. But in TFTM the inside of his chest completely changed as it explicitly showed him having a chamber to house the Autobot Matrix of Leadership.
There are NO such contradictions between BWII and BW. You need to show me something that is explicitly contradictory, not just something which exists in one story but not the other, because that alone isn't necessarily contradictory. An example of canonical contradiction would be like in the ending of Code of Hero where we see the original Rattrap cremating Dinobot's body, even though he should have been a Transmetal. This was obviously an animation error, but it still creates a visual contradiction in continuity.
P.S.: For the sake of argument, let's say that BW Optimus Primal and BWII Convoy are from different continuities, I'm not sure if this necessarily explains the separate numbering between MP32 and MP38 considering that MP08-X King Grimlock wasn't assigned his own separate number over MP08 Grimlock, and MP08-X is explicitly meant to be Grimlock from the G1 Marvel Comics (Earth-91274 to be precise), whereas MP08 Grimlock is meant to be Grimlock from the G1 cartoon universe, although the interchangeable eye colour gimmick means that he can also be from the G1 toy universe or any other universe with toy-accurate art.