Just wanted to chime in that I've encountered the exact same thing, although it's a relatively recent thing... I think it happened when I ported to 4.5 from 4.2.
The only solution I've found, pain in the neck that it is, is to create the destination directories on the source box. That keeps pkg_create happy, and the proper files are still picked up from the where they're specified by SRCDIR.
I meant to raise this a long time ago, but I got busy, my package creation box was set up so that pkg_create didn't complain, and out of sight = out of mind... :-)
Cheers, DMK
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