I did it with ReiNX payload that has exFAT support for 4.1 and it's working great.I also did the update without burning fuses guide for 3.0.1 to 5.1.0 and got this in the hekate_ipl.ini:
Code:[LayeredFS] kip1=modules/newfirm/loader.kip kip1=modules/newfirm/sm.kip kip1=modules/newfirm/fs_mitm.kip kip1=FS510-exfat_nocmac_nogc.kip1 atmosphere=1
Of course you should have FS510-exfat_nocmac_nogc.kip1 in the root of your microSD card (but you should have that already if you followed the guide).
I cannot confirm that the GC actually has not been updated as I haven't gone back to 3.0.1 and tested, but it boots fine this way and everything works.