I have a SCSI disk working under DOS, but when I boot NetBSD using the
   GENERIC kernel, or one I have configured myself, I get errors/warnings
   about being unable to map pin A [...]

You need to configure an IRQ for the card using the builtin BIOS.

   as well as some not configured warnings

Those are for devices that the kernel has no specific knowledge of.
One is the host bridge; the other is a VGA card.

   Is there some reason I get the eisa configuration message below ?
   I don't particularly want eisa configured AFAIK.

Then there shouldn't be anything wrong with the kernel telling you it
didn't configure it.  B-)