what can I do (if anything) to make sure that all steps in the module install process invoke /pkg/alt/bin/perl instead of /usr/bin/perl ?

Move /usr/bin/perl out of the way to identify the culprit(s). Another (brute) option would be to run

perl -pi -e 's|/usr/bin/perl|/pkg/alt/bin/perl|' `find . -type f`
[download]

in the package directory. Maybe both? since Qt could have some perl stuff involved in the build, or your tool chain might not be fully OS-perl-clean (autoconf/automake/configure come to mind)...