Isabelle doesn't realize she's not cis until she's already been exploring her gender for years, and at most she considers herself sort of a weird gender-fucked mess since concepts of cis, trans, and nonbinary are all kind of foreign to her. At first Isabelle conceptualizing herself as "not exactly a woman" is because of how she dehumanizes herself, but when she's in her mid twenties she realizes there's more to it than that.

As for when Isabelle starts exploring gender, she's liked taking male roles in games since she was a toddler. Sometimes she's a princess, sometimes she's a prince, sometimes she's a horse. She started actually aiming to look like a boy when she was a preteen and experiencing puberty, trying to stave off dysphoria and the body issues her trauma was giving her. This is part of why she cut her hair short when she was eleven, and why she tried to dress masculinely when Alec wasn't there to interfere. In general, it becomes more considered and deliberate with age, until you get 26yo Isabelle referring to himself as a manwhore.