32bit tga's are only neccessary if you use the alhpa channels. 24bit is ideal.
jpeg compression looks lousey (geek gfx joke) and doesn't beat a max compressed tga with winzip. And you are correct that the image is decompressed as a jpeg to take up the same amount of memory in the video card the same as a tga.
Allot of the Id engine games use tga's now, except jpegs that they really don't care about for quality. I'd say save as tga's and let the mapper convert to jpegs if they want to.