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Err, SS2 shouldn't edit that location in any way. The mod team mostly avoids that. I had some very minor texture break in one place in vault 95 but that could be vanilla.
i hade to stop using https://www.nexusmods.com/fallout4/mods/34209 because it was messing up cells and had lot of dirty code in that messed up cells all over the commonwealth as well as far Habor , and ss2 is loaded with new made cells so cant rule it out and have to ask
As a work around, you can use console command tpc to toggle pre-culling. That has always fixed that issue for me. Just don't forget to retoggle the setting when leaving the area as I read it can cause performance degradation.
SS2 actually does edit the interior of the Museum of Freedom, technically - by placing an 'easter egg' of a damaged flyer for ASAMs in the spot where they were found in SS1. That's all, though, and that wouldn't cause the issues shown in the video above.