The typical bk-based workflow for NTP developers is to start with a clean clone of the repo which does not contain any libtool .m4 files or autotools output, and run the bootstrap script to bring the repo into a similar state as one would get from an extracted make dist tarball. bk doesn't have branches, so we typically always have a 'clean' workspace to start, as each "branch" is another copy of the repo.
It occurs to me we might avoid issues along these lines by having our bootstrap script invoke libtoolize before autoreconf. Does that sound wise to the two of you?