How many people bought FS2 and didn't play multiplayer?
There are also plenty of people who bought FS2 and never looked in the tech room intel section. Does that mean that the material there is questionable?
You'll note I didn't say, I said it was possible. Look at, say, Halo co-op; does that mean there were 2 Master Chiefs? Of course not.
Okay, but in the FS2 context, there is certainly nothing wrong with having multiple player-controlled ships or anything else the MP co-op missions bring to the table.
I'd say it's as much an example of technical limitations in writing AI. Now you're being silly, anways. If the single player game isn't setup to tell the story, why not just have a bundle of standalone missions?
I think you're the one being silly by making nebulous statements about the campaign being a story and the MP missions not being so.

The point I'm making is that you can't just say that things were added in for gameplay balance and are therefore not canon, because that is also often the case with the campaign missions. Just about any canon material could be disputed if we started thinking along lines like that.
Well, I believe you've just made an assumption there in that 'it's certainly compatible with the story'. And I believe Goober already pointed out an inconsistency with regards to a Deimos 'launching' fighters. Or, for example, even the Templar contains an inconsistency, referring to 'Scarab stealth prototypes', when the Scarab is already the name of an escape pod class.
I mean, there is no obvious reason why it shouldn't be (it could work in theory, like I said). Anyway my assumption is better than what you were suggesting, that Volition may have put it into a multiplayer mission for no other reason than that it wouldn't fit in any singleplayer one.

Regarding the name inconsistency, it's no different from the GVFr Nephthys in the final mission conflicting with the GVS Nephthys class. That doesn't mean we should disregard the entire FS2 campaign as non-canon. As for the Deimos launching fighters, could you refresh my memory on where that occurs? I can't seem to remember it. Although I'm not sure that it's any worse than the tech room explicitly saying that the Mentu has anti-capital beams when it clearly does not.
The fact is that there are minor contradictions in all of the Volition material. That is no reason to discount everything they are contained in.
I believe it's worthy, again, of an examination as to whether compromises may have been made to balance multiplayer gameplay. Is that really that unreasonable?
Yes, I do think that is unreasonable if you're restricting your analysis to multiplayer missions only. If you're including the campaign missions and any other Volition material, then there is nothing wrong with that.