> They are used for the same thing, they share etymology, but they are not the same letter.
That second quote applies equally to Ä and Æ.
The variations on characters which have been merged are usually even closer than that. More like the single or double storey "a", or the single or double loop "g".
I think what you're missing is that Han unification never particularly concerned itself with whether characters are "the same" or not. Somebody basically just decided that some differences were important and others weren't. I mean, the difference between 語 and 语 is analogous to printing and cursive, but for whatever reason it made the cut. Meanwhile the SC and TC versions of 骨 are approximately mirror images, but to show you I'd need two different fonts.
Anyway the merged differences are not just analogous to different fonts.
By the way, Unicode is about scripts, not languages. If we started distinguishing by language, we might need to start remembering that china doesn't have a single language. Duplicating all those characters again to cover Mandarin and Cantonese and Wu and Hakka and Hokkien?
Should we have a different letter for Æ in Bokmål and Nynorsk? How about Riskmål?
The equivalent of Æ and Ä in Han scripts have not been unified. The equivalent of a in Futura and a in Verdana have. There's tons of chinese characters, so a few of them are bound to be borderline and maybe contentious. But overall, Han unification was unavoidable for a project like Unicode.