tpcview takes account on rendering alpha-channel with the diffuse/texture, so that black area appear transparent there as it's applied with alpha-mask purposed for envmap in-game, if I call this matter correctly.
Therefore, I don't see any issue regarding tga2tpc's TPC end-result -- particularly in this substance.
There currently no graphical editor available for editing maps yet, however there is one in the works. If you want to edit where things are in a module (map) you'll need to edit the .GIT file assosicated with it. You'll probably want to look for tutorials or ask around on the forums/discord.