There was a bit of a debate on this a while ago, but here's my two cents.
ZUN says that if there are contradictions between PC98 and windows, accept windows. However, PMiSS is also known to be not 100% accurate.
No one except Akyuu has ever mentioned Alice being human. No one's ever even alluded to it. It's not in any official profile, it's not in any print work, there is no evidence EXCEPT Akyuu's word. It is entirely possible that Akyuu is just wrong. It's happened before.
On top of that, there's tons of evidence that PC98 Alice = Windows Alice.
Firstly
ZUN actually said they are the same person. Secondly, they share the same abilities. I don't know why everyone forgets, but in MS stage 3, Alice used fairy-like familiars just like Windows Alice. In Windows canon, Alice is stated to be wary of using her grimoire due to it's power. She
can use it, she just chooses not to. Hell, her Perfect Cherry Blossom profile says that she's a versatile magician, and only recently gained an interest in dolls. This whole "PC98 Alice is a grimoire user but Windows Alice is a doll magician" is just silly. Both versions of Alice have used dolls in game, and both versions can use the Grimoire.
Thirdly, there are multiple in game references to Alice and Reimu/Marisa having a history, alluding to MS. I won't go into the details, but just read the PCB dialogue.
Lastly, and this is a bit of a meta example, but in Soku Alice uses Grimoire of Alice as her theme.
Too many people just assume "Windows Alice is a human-turned-youkai but PC98 was born and raised in Makai therefor PC98 isn't valid." That isn't necessarily the case. It's way more blurry than that. It's not only possible, it's plausible that Windows Alice was never human in the first place.
Now on the flip side I'll admit; generally when Akyuu is wrong, it's made obvious. Usually there's an obvious reason as to why she'd be wrong, whether it's because:
- Youkai give her bad information
- She has obvious reasons for being misinformed (such as in the Lunarian's case)
- She openly admits to speculation (such as in Sakuya's case)
This isn't how it is with Alice. There's no obvious reason for Alice to tell Akyuu she used to be human. There's no reason for Akyuu to assume that Alice used to be human. And in context, it wouldn't make sense for Akyuu to provide that kind of information if it were just speculation.
Another thing we have to keep in mind. ZUN's stance on PC98 has flip-flopped dramatically over the years. Sometimes he says it's absolutely canon, sometimes he says it's absolutely not, his latest statement was "it's canon as long as it doesn't contradict Windows" IIRC. It's entirely possible that ZUN originally meant for both Alices to be the same back when PCB was released, then changed his mind as the series progressed.
Because it's so blurry as to what we can trust and what we can't, there very well might not be an answer. As someone said in another thread, Gensokyo isn't real. ZUN might not have thought of a history for Alice, or he might have thought up one and changed his mind later on. The pieces might not fit together.
Personally I choose to believe that both Alices are the same and Akyuu is just wrong for whatever reason. I believe that because, besides this whole Alice thing, there are no contradictions between PC98 and Windows. But that's a rant for another time.