Because of the way Hypothesis just exposes a single test function, pytest just runs its fixtures once for that function.
This is a long running problem with Hypothesis's interaction with pytest and there is an open bug about it on the pytest side too.
Fixing this is tricky. The fixtures-integration branch has a partial prototype which makes some progress towards making it work, but it's very far from complete and has a number of issues which are likely to need substantial work to fix.
I am currently seeking funding to work on this ticket and it is unlikely to make much progress without said funding.