Daniel, GNU Hello is written to be an example GNU package, that is, to do things in a recommended minimal-future-maintenance way. Therefore it uses Automake and Gnulib, among other things, and the top-level Makefile.am is as simple as possible. There is no way to insert such ifndef's even if I wanted to, which I don't. Sorry.
It sounds like your project simply won't work with the way Gnulib is written. If you want to discuss that, [email protected] is the place to do it. Best, karl
