i like to keep my system clean so it's a good thing that packages which
   are installed from pkgsrc are in one place and don't mess up with
   locally installed packages (which i happily narrowed to absolute minimum
   of two packages, which have local patches so then can't be submitted to
   pkgsrc, and few small scripts).


there are really easy ways to keep extra patches for pkgsrc for your
use.  i can't remember the new/better way that lets you keep it out
of the pkgsrc tree entirely, but you could always have a
patches/patch-local-foo file (at least for a long time now.)