Yes, to flash the system (with that I mean the whole original ROM) you need Mi Flash Tool.How did you flash system?was it thru mi flash or? I tried flashing new stock rom thru mi flash tool but not successful,I did not flash any TWRP, just normal patch boot and this really happened after magisk update
When I did it, I found only the older 10.0.9.0 ROM, not any newer ROM. But anyway after you flash it, you can do the update in the settings, you will get the newest system (October Update, I guess) then.
Only after you flashed the ROM you can flash the patched boot.img to get back root and after you can flash magisk through on-the-fly-TWRP.
The Stock ROMs for fastboot (Flash with Mi Tool) you can find on the***********.com.