Objective Development Forums

The readme recommends that AVR-Doper should be used in HID mode with avrdude. I wonder if it would be possible to use AVR-Doper as AVRISP mkII clone with new firmware, to be able to use it directly from AVR studio.

No, at least not easily. The mkII USB interface uses bulk endpoints. And bulk endpoints are the problem why serial emulation mode is somewhat instable.