Do you use OpenMW? I had this issue on OpenMW, but not in my current plain Morrowind installation. I'm wondering if the issue is due to OpenMW or due to a mod that I installed alongside this one.
Confirmed OpenMW issue. I opened it with Blender, the collision vertices seem really messed up, or the original game engine handled them differently. If you delete in_common_lighthouse.nif, the lighthouse still looks awesome, no hopping required.
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edit: I think I did it right though.
Thank you for this awesome mod!