I am in the same boat as you, with family from Bari (nearly all Modugno, but for some reason my grandfather was born in Giovinazzo).
I am thinking there must be some pre-Napoleonic era records available, at least in the province of Bari. The reason is that some of the marriage records I am finding from the early restoration period (1815-1830 or so) mention the filing of additional documents (the allegati) including birth records of the bride and groom and death records of the parents, some of which occurred prior to the Napoleonic Stato Civile establishment.
However, they're generally not in the Antenati online archive, perhaps because they may have only been filed locally and not in duplicate like the other documents that were sent to the state archive, but that's purely speculation on my part. I was in Modugno last week on a trip to Bari and Basilicata but didn't have time to stop by the comune Stato Civile to test that theory. They do have email addresses so I might try inquiring about marriage allegati for those older marriage records.
And I wouldn't say that pre-1800 church records are scarce. It depends on the church but most towns have a "big steeple" mother church, so I would start my church inquiries there. Even little Modugno (granted, not as little as it used to be) has records in its main church that go back that far.