You extract the contents of the factory image zip file into a folder. The extracted folder will have 6 items (see 1st screenshot below). You place these items in your Platform Tools folder and then run flash-all.So if I am trying to flash this. Am I only to use the extracted folder? Also extracting the boot.img Am I removing it entirely from the extracted folder? or do I leave the stock boot.img in the extracted folder? Then flash all.. Then I proceed to flash the patched magisk boot right?
In regards to patching the boot image, the boot image is extracted from the zip file shown in the 2nd screenshot below. You then patch that in Magisk, go into the bootloader and flash that patched image.
And of course follow the instructions in the OP about modifying the flash-all.bat file.
And if this is the first time you are disabling those 2 flags in vbmeta you will have to factory reset after disabling those flags and proceed to follow the instructions in the OP. A search will reveal several threads explaining this if you are unfamiliar with it.