Nice to see someone else using the Arduino development platform. I guess
you know more about Debian than I. The Ubuntu repositories have the
Arduino IDE and that is what I use. I have had more problems with the
Atmel programmer than an Uno board when trying to connect. The problems
I have had there was in permissions on the USB device. Having tried on
many occasions to set these permissions and failing, I simply start the
IDE from a terminal using sudo when trying to program a new processor
for proto board use. The only issue I have had doing this is saving
sketches to my home rather than the root home. I know I could buy chips
with the boot loader already programmed to lighten my load, but I would
rather not use an outside crystal so take that extra effort.

Closer to your question. I am thinking the port differences has to do
with the actual com port on the arduino and the programming port on the
arduino. I could be wrong on this however. I do know that a programmer
issue with permissions has something to do with that. If you want to
experiment much with the arduino note that using the wrong ports for
power control can brick a processor. Something I have done many times over.