Missed this thread until now.
I'd favor the tp2 in the mod folder being executed with higher priority than a tp2 in the main game folder.
tp2 inside the mod folder is nowadays standard, but old mods cannot be shipped with the tp2 in the mod folder instead of the main folder because risk is players forget to delete the old one. BG1NPC Project v20 still ships the tp2 at mod folder level because of this, for example. I had a very, very stupid "bug" on my own mod install because I didn't think of an old tp2 still being present in the game folder that took me way too long to realize what is going on - my own mistake, I know, but this is what could happen to some players.
I am definitely for shipping the tp2 inside the mod folder as it decreses the amount of files I have to move around when testing mods in my x+ BG installs, so this request would be something I second.