Now I am using -
./configure --prefix="$PKGPATH" --bindir="$PKGPATH"/localbin
as the general compile options, PKGPATH would be /app/xarchiver if I were building from source.
Sure, many of those binaries in /apps/extname/localbin, or /apps/extname/local/bin could be removed to save space if they are not needed. I imagine xarchiver would need those archiving binaries contained in it. I tried to remove some binaries out of filezilla to save space, but the extension was then broken, though I am sure some could be removed.
Using --prefix=-/apps/extname/local would also prevent conflict, but I would have to redo the buildscm script to accomodate it, which I may try to do so it is an option. There are ongoing improvements made to the scm format that are not yet reflected in what is available in the repo. In time, it will become more standardized.