Thanks @ptillisch and others:
Sorry I missed noticing that you did split this out from the other thread. Which makes total sense!
I thought I would bring over some of my other thoughts from that thread. Some of which I think have been covered:
That is, before that the ESP32 probably has conversation with host, and suddenly the RX/TX pins going to the USB connector are changed. How is that handled. Is there some form of USB reset issued?...
Also if you currently compile for WIFI, it has no USB support built in? how does that work. Serial object is still trying to talk to ESP32 through their UARTs
Now if you hack platform.txt to remove the NO_USB setting, then the UART to SerialX objects are probably messed up. Where Serial1, probably tries to talk to the ESP32, and Serial2 probably talks to pins 0 and 1... Could be wrong.
Where is the USB Descriptor defined?
What about bootloaders? If solder jumper in place, do you need new bootloader? Probably not the same one as MINIMA, if for no other reason, the LEDS (pin 13) are on different IO pins on the two boards. P111 for MINIMA and P102 on WIFI.
What does double click on the reset button do? I am assuming that the ESP32 sees it, and probably resets the main processor...
EDIT: I meant to then say, but creating a new variant should solve many of the above things 
Here is a thread I started awhile ago, that @ptillisch gave me a lot of good instructions on how to do this:
How to build and change the latest core sources? - UNO R4 / UNO R4 WiFi - Arduino Forum
I still wonder how the switch over from the ESP32 is controlling the USB and suddenly the other processor has it, is handled. Maybe the processor detects USB is available and does a USB reset? at which point the host will query it for it's descriptors and the like?
Will be interesting to try! Wonder if I should have a 2nd WIFI board...