It’s not so much an issue with software, Hekate works great for this purpose, the issue is if you connect an EMMC module to a console and the EMMC in question is on a higher FW version than the CPU count (of the original paired FW version) you burn the fuse and you can’t stock boot, this is not a huge issue as you can recover quite easily on an unpatched console, but this becomes a small nightmare on a patched/Mariko boards as you then require a modchip to load homerew.
Though as I say, all the above is a non issue if you boot straight into hekate from RCM, you can’t burn fuses here, it only happens when the console boots stock.
The issue on the PC end alternate backup method is more down to the device which allows you to connect the EMMC module to PC, the device powers the 1V8PDR line on the EMMC (VCCQ) at 3.3V… while most EMMC ICs will tolerate this, it is out of spec, but as this line was previously dodgy I can’t recommend using this device.