So it looks like I've answered my own question.
The problem I was having isn't with core-perl per se, but to some degree with ExtUtils::MakeMaker, and also with some CPAN modules (especially those with multiple Makefile.PL's, when command-line args are not passed along).
In the end, the easiest fix was simply to hack Config.pm to reflect the new location of perl in a few parameters. Not ideal, but to truly get it to work would require a lot of changes in a lot of modules.
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