I think either one will do. 'Chan' is used as an honorific title for younger girls, 'San' is polite in a more general sense and 'Sama' is mostly used for people with higher status than you. Phase-chan is very cute though!! :3
Well of course she is an human and a female, these elements have nothing to do with the way how she was created (on the opposite they are debatable for Alpha 152 taking in regard her singular nature).
I really hope that she will get some true love in the future of the story, I would like to see Kasumi consider her as a sister (after that Phase 4 will eventually change side).
Actually, the gender doesn't seem to be debatable for Alpha too because she has breasts and get's a schoolgirl outfit in LR.
Species is, because I can also let my cat or dog wear a skirt (Some people really do I heared). Although one shouldn't jump to conclusions from clothing.
Well, actually the gender is something related to the sex of the subject: if Alpha-152 has really no reproductive organs/apparate (how her model in game seems to suggest), then it should be considered technically an "it" despite any other things (female breasts or outfits).
If something Alpha-152's gender is IMO debatable because previously she was a female (human too), according to the new canon that see her being a mutation of the original Kasumi Alpha.
Kasumi-san. I'm sure she would tell them that's her name. And I'm sure if people knew she was some science project, they'd just refer to her as Phase-4 (prolly not to her face, thought).