Technically speaking, you can't use the original files for anything other than what they were intended for. There is a loophole concerning fair use in derivative works (aka fan fiction, aka what we are doing here).
And TBP did replace most files from FS2 with homegrown versions. There might be a few from retail FS2 left over, mostly in the interface.
That said, if you want to use retail assets (like the interface) in a mod, you don't need to copy anything. If you read about how FS2 modding works, you will see that the retail assets are always available to you.