剛po完沒多久就找到解決方法了
把skyrim.ini的Archive多加HighResTexturePack01.bsa及HighResTexturePack02.bsa就可以把官方材質包當作預設的bsa檔載入(esp就不用選了)，材質mod就不會被覆蓋過

[Archive]
sResourceArchiveList=Skyrim - Misc.bsa, Skyrim - Shaders.bsa, Skyrim - Textures.bsa, HighResTexturePack01.bsa, HighResTexturePack02.bsa, Skyrim - Interface.bsa, Skyrim - Animations.bsa, Skyrim - Meshes.bsa, Skyrim - Sounds.bsa
sResourceArchiveList2=Skyrim - Voices.bsa, Skyrim - VoicesExtra.bsa