Hello,
selecting "JTAGICE3 JTAG" in the arduino IDE and trying to burn the bootloader results in an error.
I tryed to discuss it on the forum before i came here but with little response:
https://forum.arduino.cc/index.php?topic=639257.0

Expected behaviour:
IDE flashes bootloader over the JTAG interface using JTAGICE3

Actual Behaviour:
IDE disables JTAG on the Target and fails flashing the bootloader

All the details are on the forum, to make it short, the first thing the ide does is set the fused to:

avrdude: writing lock (1 bytes): 0x3F
avrdude: writing efuse (1 bytes): 0xcb
avrdude: writing hfuse (1 bytes): 0xd8
avrdude: writing lfuse (1 bytes): 0xff

Which disables JTAG. Since this happens right at the start it obviously can't continue flashing the bootloader.

What i suggest is leaving the JTAG fuse active when starting the "burn bootloader" process and possibly not disabling it at all.