Seems strange to me that bin and lib files would be hardcoded. Share often is hard-coded because, contrary to the name, these files are not typically shared between applications. I'm not sure if there is an include path already set, as there is with bin and lib, but in any case it can be set with CFLAGS and similar. Then again, maybe these dev files were intentionally made to not be overridden by external programs, but that seems a little strange for a Linux system.
I feel pretty confident that I could at least move the files from /bin, /lib, /usr/bin, and /usr/lib into /usr/local/{bin,lib} without problems, and repackage the remaining files into a much smaller archive. If I break something I still have most of my TCE files to repopulate tclocal, so maybe I try that.