Arduino clone CH340G (ATmega328P), MIDI over USB
V-USB bit bangs some GPIO pins so that they speak the low-speed USB protocol.
This does not use the 'normal' USB connection through the CH340; you would have to solder a separate USB cable to those GPIO pins.

Programming would be no problem; the V-USB code is just normal code that runs on the MCU. (Programming through ISP pins would be required on hardware where USB communication and programming is handled with a second AVR MCU; in that case, the USB/MIDI code would run on that second MCU.)

Low-speed USB is not supposed to be used for MIDI, and as a software emulation, V-USB does not work very well, or efficiently.
If you want to create a USB device, you should use an MCU that actually supports USB in hardware, such as the ATmega32U4 or AT90USB646 used on some Teensies.