As of right now I have found one thread that treats specifically of the issue I am having and there doesn't seem to be a solution for it without relying on a query, which is a no-go since I need it to be automated through PyQGIS. Here is the other thread: QGIS topology checker - check if point features are covered by line features

I tried the Topology checker myself on a project which I made sure almost every point is snapped to lines and it has strange behavior.

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Fo instance, here, every line end (so start_point and end_point of each line geometry) are snapped to points. Yet I still get errors. The only line that doesn't return an error is not preexisting in my project and I added it myself as well as the extra point it is snapped to.

I fail to understand whether I'm misunderstand how to how to use the topology checker or whether its meant to be used in other cases. Here is the rule I used:

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