Arduino IDE won't use selected port
You mean that the STK500 v2 programmer uses an emulated serial port
rather than direct USB? Then I guess there is a bug in the Arduino IDE.
The file programmers.txt contains the following lines
describing the programmer:

avrispmkii.name=AVRISP mkII
avrispmkii.communication=usb
avrispmkii.protocol=stk500v2
avrispmkii.program.protocol=stk500v2
avrispmkii.program.tool=avrdude
avrispmkii.program.extra_params=-Pusb


You may locate this file in your Arduino installation and replace the
last line from this snippet by

avrispmkii.program.extra_params=-P{serial.port}


If that works, it would be a good idea to submit a pull request with the
fix to the Arduino team.

Alternatively, you may try selecting “Atmel STK500 development board” as
a programmer. This is supposed to autodetect the version of the STK500
protocol, and uses the correct serial port.

Edit: you may also have to replace

avrispmkii.communication=usb


by

avrispmkii.communication=serial


C.f. this bug report, which seems to cover the exact issue you are
facing.