Maybe it's because Alice is (my favorite character and) the one character I've probably spent the most time thinking about, consciously or not, she seems particularly nuanced even among the touhou characters to me.
You brushed on it, but to put it tersely, I'd say the one driving factor that underpins Alice's whole character is obsession. On one side, a sort of creative obsession towards her craft, like you said. Gathering knowledge isn't so much the end goal so much as it is simply a means to further sharpen her own skills towards her art - making dolls. All this is fairly easily visible but the other half of her that gives her character a lot of conflict and depth is something that often comes hand-in-hand with obsession - perfection and perfectionism. I don't think you can really be an obsessed creative type without always striving higher, for more mastery, for more knowledge, for greater
perfection. And with this perfection comes a sort of inevitable disappointment that takes its form as the melancholic side of her character. In what I think might even be a subconscious decision for her, she imposes self-restrictions on herself. In a strange way, it ends up being that she plays by her own rules and never crosses any lines she draws for herself. This can be seen in how the canon material says she never displays her true strength and what not, something we all know and heard a million times. It seems to me to be a kind of subconscious protection-ish mechanism to suppress potential disappointments. The self-imposed restrictions can be used as excuses to herself to avoid disappointments. I think she's weirdly very emotional this way, very melancholic, in a way that is very contrary to what I'm seeing blue as defining that makes me struggle to keep her categorized here, even if it is the most appropriate surface-wise.
As for the cruelty streak you mentioned, I think it's more of a display of her assertion as a creator. It strikes me as a sort of particularity, an obsession if you will, that she shows that only she has the sole right to destroy her own works -- and not anyone else -- as their creator. Seen this way, it can almost be a sort of show of affection, a weird display or form of love, for her creations to be the one to destroy them, by her own hands, just as she was the one who created them. It was a possibility that struck me after this one time when I woke up in the middle of the night, left the dorm, and built a giant snow moai statue out in the middle of the school campus after a very rare snowy day. Then the next night I woke up again midnight to go knock it down before someone else or the warming weather did. It might almost be contrary with her popular depiction as motherly (a mother-alice), and though I certainly do see shades of that in her character, I think she at times more strongly shows a creatorly romantic notion (a creator-alice). And it's these weird sort of romantic sentimentalities that she shows that make me hesitant to keep her true blue, but at the same time I don't know what color this would be. Neither red nor black nor white seem to show this weird perfectionist romantic sentimentality as far as I'm reading up.
Well at least, that's how I understand and relate to alice's character, and a couple of the reasons why she's my favorite. (which is to say, I'm not asserting that this is how she is, obviously)
e: I forgot, but her destroying her own dolls that she must have put lots of effort into can perhaps be another display of her own inner conflict, a venting of the stress, creative or otherwise, that comes from her passionate obsession and perfectionism. Again, conflicted melancholy, but it doesn't really seem that black.
