There's no issue de jure. Transnistria is an autonomous territory inside Moldova and EU recognized it as such.
There is the de facto issue of said territory being unruly, extremely Russian-friendly and host to actual Russian military.
That issue won't stand for long however once the ball gets rolling. Moldova has already begun increased strategic cooperation with EU and if the referendum passes and Sandu gets a second term I expect there will be a referendum for amending the Constitution. If that passes, Moldova will be able to ask for military help outright, which will clean up Russian presence in Transnistria in short order.
Historically speaking I remind you that most prospective EU members have worked towards NATO membership and usually achieved it even before joining EU.