I did some quick testing on my own patchpack but was not able to reproduce this. Looking back I'd already made a change to address this here: JGRennison/OpenTTD-patches@92c48d6, reverting this change causes the desync behaviour above and output from CheckCaches.
If this general approach is acceptable I can turn it into a PR.
This could result in stations being incorrectly added in the case of
non-rectangular industries where the station's catchment only
intersected with a non-industry tile subset of the overall rectangular
This could cause multiplayer desyncs.