I mean to say we are not ontologically motivated.

Who's "we"? Lesswrongians seem pretty motivated to assert the correctness of physicalism and wrongness of dualism, supernaturalism,, etc.

The examples OP gave aren't ontological questions, only questions with ontological implications, which makes the ontology descriptive rather than prescriptive. That the implications carry forward only makes the description consistent.

I'm not following that. Can you give concrete examples?

In the scholastic case, my sense of the process of moving beyond Aristotle is that it relied on things happening that disagreed with Aristotle, which weren't motivated by testing Aristotle. Architecture and siege engines did for falling objects, for example.

What I had in mind was Aristotelean metaphysics, not Aristotelean physics. The metaphysics, the accident/essence distinction and so on, failed separately.