I see what's going on a little better. The filepatch /usr/share/python/runtime.d/libpetsc3.6.2-dev.rtupdate is common to all arches, but its contents are architecture specific, which breaks Multi- Arch:same.
Since that file was generated by dh_python2, it indicates that dh_python2 is not [sufficiently] multiarch aware. Perhaps related to bug#798491. But the actual python scripts themselves (.py in /usr/lib/petscdir/3.7.4/x86_64-linux-gnu-real/bin) don't seem to be architecture specific. I wonder if it makes sense to split them off to a common /usr/lib/petscdir/3.7.4/python dir.
