This is one of the few instances where my answer is kinda boring and I don't have, like, a stringboard to whip out. I've always headcanoned that the blonde is just a dye job. The reason it's not completely grown out already the time Extinction rolls around is because, in the midst of her loner misery between films, Alice decided to treat herself by re-doing the blonde. But I suppose you can easily come up with some sort of RE 5 Jill-style explanation where repeated exposure to the virus caused her hair to turn brown over time. If T-Virus can genetically alter her in such a way that she can blow up/move shit with her mind, who's to say it can't change her hair color, amirite?

Alicia Marcus has brown hair as a child, though, so dye's always made the most sense to me. However, I'm not opposed to the idea that some clones end up with little genetic quirks. For instance, I HC Bad Rain has naturally straight hair, but the real Rain's is naturally curly. That could also explain why many Alice clones we see are still blonde if Alice is naturally brunette, but the blonde clones we see in Extinction have a different hair color by the time Afterlife rolls around... Maybe Isaacs could never recreate Project Alice because he kept giving those clones some Umbrella-branded bullshit that temporarily altered their hair color. Maybe that's what one of the many tubes fed into them in those bubbles was for lmao