I think the issue is that it would, in some odd sort of way, disregard the autonomy which the games ostensibly gave to you. It's not all about shipping, because I'd feel the same way about character deaths (though most people don't ironman so you can more safely assume everyone lived). Part of the appeal of Fire Emblem is having control over who lives, who levels up, and who marries who. If games want to have canon pairings out of the gate (like Shadow Dragon), I'm fine with that. But it's weird to give me the option and then say it doesn't matter.
I do disagree that this is "rare" though. FE10 assumes everyone in FE9 lives, FE3/12 assumes no deaths in their prequel, etc.
I don't think it impacted Thracia sales either, but I can imagine that, where I invested in FE4, it would be weird or even off-putting to see all those choices ignored. They're separate games, but it makes it Kaga's fanfiction more than my playthrough, which is weird.
In this since, I actually favor the FE7 approach (as loathe as I am to praise the game). Or at least the reverse approach, since it's a prequel. If a pairing in canon in FE6 (like Bartre and Karla), it's canon in FE7. Things which can change in FE7 aren't canon/specified in FE6 (like Wolt's father). In a game so full of retcons, I respect that attempt, though I would appreciate if FE games instead put games within the same universe sufficiently far apart that it wouldn't matter whether Radd married Laim or not.
This is also coming from the perspective of someone who replays these games with different units and different pairings, so I'm not totally attached to any vision of what it "should" be. Then again, I'm also used to these things not being set in stone.