Correct, the option "skip confirmation" in AIO helps, if touch is not working and you want to install AIO tweaks.
Regarding your previous Edit #2:
If you do not install the ID7/Autorun tweak prior to the FW update, then yes, you will loose the ability to install tweaks, once 59.00.502 or higher is installed. From 59.00.502-70.00.100 you can enable the system to install tweaks via usb again via serial access only:
www.mazdatweaks.com/serial
If you stay at FW v55 (and do not update to FW 59 or 70), you still have the ability to install AIO tweaks via USB.
I think the ID7, aka Auto Run, is what will allow me to always be able to just use USB without having the need to serial port.. correct? -> correct. from 59.00.502 up to/including 70.00.100.