I don't see the need for a debugger in a final product.
Surely you install your firmware into your product via an external programmer (or native bootloader if the chip has one)
You can install your own DFU or OTA loader for any subsequent updates.
You only need the debugger when you are developing in the first place.
Of course you may be intending your boards for a class of 250 students. In which case you do a deal with a manufacturer for their "evaluation boards".
It would be interesting to know how many Zero / M0 Pro boards were ever manufactured. I suspect they are quietly retiring the Zero. But it would be better to just say so.
Incidentally, the SAM JTAG header on ATMEL-ICE is wired backwards. (which seems CRAZY)
David.