There is a lot of history around USBSerialEdit - fixed my comment above about trying to use USBserial.
We (well actually I ) got rid of its usage in the sketch, as it was non-standard.
When Leaflabs wrote the libmaple core, none of the AVR boards had onboard usb serial, so LeafLabs for some reason chose to call the serial over usb by a different name.
But in 2014 when I looked at it, in the light of the AVR Leonardo and the Due, it made more sense / more compatibility to map the Serial USB to Serial for the Maple mini.
I agree it can be confusing, that the upload method changes this, but I assumed that if you are using an external device to upload that inherently has serial i.e a Serial to USB converter or the BMP, then it makes sense to assume you are doing this for a reason and want to not use the onboard USB
The confusion is that the BMP does both. Its both a debugger and also has Serial USB.
STlink does not have USB Serial, so it made sense to enable it for STLink.
So, yes it can be confusing, but I suspect its because you are using the BMP if you were using STLink you'd not have noticed a conflict