Dear @Wobaffet
Please accept my apologies for the delay on my response. I really appreciate your patience.
After I research internally, here are my points:
-Yes, you can burn fuses via UART by using MCU Boot Utility. These pins are the one have to be configured:

In addition, do not forget to configure SW8 to 0001.
-Of course, no need to use bus isolation resistors due to the reasons you mentioned.
-And yes, you can only use UART or USB for flashing the QSPI Flash.
Hope this is helpful! Please let me know if you have some other questions.
Best Regards.
Pablo Avalos.