I've done both, but in either case, compiling your own Perl is the right approach because in the long run, each application should get its own, independent Perl binary. At least unless you can maintain a comprehensive test suite and test environment to ensure that module and Perl upgrades go smoothly, decoupling applications from the Perl version seems to be the best approach to me.

Compiling your own Perl isn't hard, the nasty thing is installing the C libraries that some XS modules want. I don't know if/how BSD or Pair Networks provide such libraries like libxml2 or libexpat - if they don't provide them in a convenient way, you might want to go with the home-hosted version.