Hey there, Kalitinsa! Thank you for your comment. This is the writer replying directly, so I hope this can help with any thoughts you may have on the game.
I'm a gay woman myself, and I have no problem with the term handsome being used for other women. In my personal opinion, this is a gender neutral term used to describe someone who is...well, handsome. Good-looking, strong, charming...these are all things that I believe factor into the word. Women and femininity are not - and should not - be restricted to the use of 'feminine' sounding words like pretty, beautiful, etc, though there are also more than a few instances in the game where the girls are also described as that. I'm sure you'll see a variation of compliments as you progress through the routes.
On a literal level (though I think this is being a bit pedantic and is not my personal reason behind why I use it), you can use it for women just fine. This was an unusual comment to receive, so I thought I'd cover my bases to be triple-sure and yes, it says you can right here.
Regardless of whether or not our opinions differ, I sincerely hope you continue to enjoy LOVE BAKUDAN!