(The 'perl Makefile.PL' step generates the xs file.)

It does not. The Makefile thereby generated has a rule that turns the supplied .pd file into .pm and .xs files, and for distributions that have "opted in" and with a PDL 2.058+, a .c file per operation (allowing parallel builds).

Probably the best heuristic to spot a PDL distro that generates XS rather than being a pure-Perl user of other PDL modules is the use of PDL::Core::Dev, and/or calls to pdlpp_stdargs.