My daughter is the same way- very strong and builds muscle mass easily, but she has to really work on her flexibility. She's eleven now, but when she was your daughter's age, she really only worked flexibility in the gym. When she started team, she started working splits at home. Her biggest struggle, though, was (and still is) shoulder flex- she'd work hard on it in the gym, but only sporadically worked on it at home. Only in the last two years has she started choosing to work on it consistently. She's made huge progress and is very proud that her coaches often use her as the example to some of the younger girls that you can become flexible even if you're not naturally so.
ETA: I forgot one of my main points, lol. I have always been big into the notion that gymnastics is her thing, not mine. If she asks me to do or help her with something, I will, but I don't push her to work anything at home. As she grew and became more aware that her lack of flexibility was holding her back, she made the choice to really work on it- but it was her choice. I did, however, tell her a couple of years ago when she was complaining ALL.THE.TIME about her shoulder flex (and was being encouraged to work on it at home by her coaches) that if she didn't care enough to work on it, then she didn't care enough to complain about it constantly.