Then you may have to split the glass into its own DFF, and map it several times in map editor. You may also have to turn off alpha transparency flag in your building DFF, because as a rule of thumb, opaque models should not be drawn last.
I recommend using Magic TXD instead. https://www.gtagarage.com/mods/show.php?id=27862
TXD Workshop is prone to errors and may corrupt data.
Guide for creating TXD
Game exporters usually ignore custom rotation/scale values and reset them back to 0 on export. Try applying your custom transforms/scale in object-level and it'll show up in the correct scale
As this question is mostly a server/scripting support question, it's been moved into a better place for best result .
We are not able to help with unlocking/decrypting server assets here - you would have to use a backup key to do this yourself.