Just tested with 6 seconds and Instant, in both cases the digital commands match the rate of the physical. This is using the on/off commands. I am using my driver linked above. I also do have firmware v 3.10 but the changelog does not mention any fixes with the ramp rate (although could be fixed and not documented).
Did one other test as well, it seems they fixed the firmware in v3, and setLevel will honor the fade if you set it. If I set the duration to 0 it will be instant, if I set a value it does the slow fade. If left blank the duration will match the ramp rate setting.
I would try my driver first see if that fixes it, if not it must be the firmware. It is possible the built in driver is not sending the on/off and setLevel commands the same as I am I, thus not getting the same results. I did some research for my last driver update to make sure I was following the zwave docs and sending all the proper commands in this area.