I think you've missed the point. Like Ryushikaze said, your logic is based on something that is deliberately present in the game to encourage replay value. Ryushikaze hit the nail on the head with the whole New Game+ argument. Part of WEAPON-D mode is where you have to rescue comrades who have been trapped in another dimension. Would you consider that the normal rescue mode is not there canon either because there is replay value to it and characters can be repeatedly detained by AVALANCHE? I understand what you're getting at, but what I don't get is why it's an issue. I don't particularly think it's canon either, but it has absolutely no bearing whatsoever on any other aspect of my FFVII experience and I don't believe it should affect anyone else's.
But, that's just my opinion.
It's not an issue to me either. I'm just curious about the story of the Compilation.
And yeah, you have a good point. Weapon-D Mode can be canon.