The archives I downloaded off of back2roots.org came with no documentation, but there did seem to be a documentation archive somewhere. I was hoping I could just be lazy, oh well.
fd2pragma is more flexible than fd2inline.
Flexibility isn't of any great concern to me since (I think) that I only need to use this program once for a specific task (to convert files from the 3.9 NDK). Whichever one will accomplish that task with the least amount of effort is the one I want to use. Since I know little about either utility I can't say which that is.
You only need hunk2aout if you want to link Amiga hunk files with gcc a.out files, but it sounds like that's what you want to do.
What I want to do is develop Amiga applications using gcc. Beyond that, the only things I know are from tutorials on setting up such a dev environment. One mentioned converting amiga.lib into libamiga.a using hunk2aout. I don't know what this library does, so I don't really know if I need to convert it (apart from the fact that some tutorial told me to do it.)