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.