Yeah dude... that's how expanded universe works. Like Boba Fett punching his way out of the SarlaccSo stupid... but it's official canon!
I never said any of this was good canon -- good or bad is a matter of opinion, and as you said it's better to discuss facts rather than opinions otherwise we'd end up going in circles. The canonical fact is that the Japanese BW canon is intended to be part of the Canadian cartoon continuity much like in an expanded universe capacity. Same with the Marvel UK comics - Simon Furman wrote them as an expansion of what Bob Budiansky was writing for Marvel US. Marvel tried to separate these two worlds by establishing Earth-91274 and Earth-120185; Earth-91274 is where ONLY the events of the Marvel US comics occur and supposedly none of the expansive material of the Marvel UK comics happens, and Earth-120185 is where everything in the Marvel US and UK comics occurs. Problem with this of course is when Simon Furman took over from Bob Budiansky in writing the US comics and started tying in Earth-91274 continuity with events from Earth-120185. For instance, the entire Matrix Quest and subsequent stories after that could NOT have occured if not for the Autobots having blasted Optimus Prime's old body off into space in a funeral barge and the whole Deathbringer story -- events which had only occured in Earth-120185! So I guess it meant that Earth-91274 was retconned as being "everything that happened in the US comics plus some stuff that happened in the UK comics that ties back in with the US comics."
As I said, you can look at BW in a similar way - different continuity streams. Let's call them Stream A, Stream B and Stream C just for convenience sake.
Stream A: Only the events of the Canadian CGI cartoon occured. Everything else is ignored.
Stream B: Only the events of the Canadian cartoon, Japanese anime and 3H BotCon/OTFCC comics occured.
Stream C: Only the events of the Canadian cartoon and the IDW comics occured.
So in Stream B we can conclude that Optimus Primal possessed a Matrix, whereas in Streams A and C he probably did not.
Sorry, I have to get ready to go to Tokyo, so I don't have time watch that... but remember that in G1 Season 1 we saw the inside of Optimus Prime's chest and there was NO Matrix and not even the housing component for it. Yet in Transformers The Movie, there it was. In the early G1 comics the Matrix was an intangible program housed in Optimus Prime's brain (which was transferred to Buster Witwicky's brain and later back to Optimus Prime) - yet later on it became a physical object inside Prime's chest like we saw in the movie.
Also, Primal's Matrix is kinda "deep" (ish) and had to come out IIRC