Pkgsrc invokes configure scripts with an explicit --hots= argument, so
running ltconfig directly does nothing useful in this case.  If you tried:

    ltconfig --host=--netbsd

you'd see the error, because this is ths (incorrect) argument passed by
pkgsrc.

This should have been addressed by a fix I put into bsd.pkg.mk yesterday.

Hmmm.  I re-sup'ped last night about 12 hours after you said you put in
the changes.  I checked and verified that bsd.pkg.mk did get copied over
so I assumed I had the new one.

I can try again later on today.
Not to tie up your time, but I could also give you an account on my machine 
and let you poke around and see what you find.  (I'm not terribly worried
about security)