Fairly clear they have not been aligned, as you say, and that either the gearbox or the rear wheel, or both, have also been at an angle to one another, causing the unequal side-to-side wear on the rear sprocket. Quite surprised that the split link or a side plate hadn't failed on the chain actually, with that degree of chafing.
You're not overthinking, but I think that unless it's 'just' a rear wheel alignment thing, you might have moved too fast towards reassembly. Think I'd want to be able to get a long straight edge across the sprockets to be sure that all is good for your expensive new bits and I don't think you can do that easily with the primary side assembled again.
I suffered from a similar set of problems with another bike, and in the end had to beef up the primary chain tensioning system to ensure the the 'box stayed straight, and rebuilt the rear hub/axle to be certain it was 'right', with new sprocket, bearings etc and spacers checked for dimensions against other bikes & whatever data I could find. Boring - but with expensive new sprockets (and also the new bearings) at stake I think worth it.
Haven't had chain trouble since, but I had actually broken two good quality chains before. The first one I put down to bad luck . . . but a second one - no way!