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Fixing window transparency only in places, that can be explored. I faced some difficulties doing this and spent more time than anticipated. Beside the transparency, I fixed an improperly placed wall and some lighting problems along the way. I did edits to existing lightboxes and added new ones. Refer to the screenshots with tags. A material is included as loose file, for easier access to the settings. The alpha is reduced to 0.90, to increase the transparency a little bit, because the texture is 1K and quality is not good due to compression. There are minor adjustments to a couple of decals, trash piles and brambles/shrubs.
The windows' nif files contained two meshes for the glass, but one of them was not always double sided. So I got rid of it, left the other mesh that was. I used existing Effect Shader and Alpha Property settings, BGEM material file. There is one major issue with this fix - when you use pipboy light, most windows are transparent, but there are a few that become almost solid color/texture under the light. More noticeable at night. Managed to fix a couple of places by separating/replacing the glass, but for others that method didn't work. It's really weird, the same window nif file is used in 5 places and at 3 of them it displays that issue. If you don't like this, a workaround I found is to disable Effect Lighting setting in the material file. It might need adjustment to other settings after that. An optional material is included, which will make the glass look dark at daylight, like the broken glass of the cars, still distinguishable at night. Not perfect, but that's all I got. Or you could play around with the material's settings yourself.
The plugin has ESL flag and yes - includes precombined geometry and precombined visibility for the edited cells.
The mod should be compatible with texture and window overhauls, just don't overwrite the material file.
It's probably not compatible with mods that edit the same cells, like mods making the hotel into a settlement. You can try running the window fix after such mods, but I don't know what the consequences will be. If you don't need settlers or food, maybe look at the Mobile Workshop by SKK. Another option is the Fallout 76 C.A.M.P..