And it kinda does, as it extrapolates on the events mentioned in the ending timeline (i.e. At the time Kojima intended to end the series with MGS4, so MPO was pretty much the only game that would've filled the gap between MGS3 and the original MSX2 Metal Gear. Portable Ops was definitely promoted as mainline game when it was first released, so there was no debating of its canonical status at first.
