How to select specific programmer from multiple when using flashrom
Looking at the source code, there is only one CH341A programmer possible. 

Supporting more than one on a PC will require you to change the source code (look for libusb_open_device_with_vid_pid(...) function call). You want to look at the serial number string before using the device.

Note that this will only work if the USB devices have unique serial numbers - you can check this with lsusb -v for example. Some el-cheapo devices do not have serial numbers or they just use the same number.