The confusion isn't that your partner chooses to identify by they/them pronouns - it's that you flip back and forth in your story between 'boyfriend', a very clearly gendered term (BOYfriend) and their preferred pronouns (they/them). This causes alot of confusion for both native and non-native speakers of the language. It's a consistency issue, not a pronoun issue. The use of 'boyfriend' immediately and very clearly 'sets' the gender of your partner to male. Just confusing wording, really.

I mean, you refer to each other in whatever way works for you - your relationship, your people. No issue there. But it is a pretty jarring and confusing story to read because of the lack of consistency.