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Handbrake is not intended to be a disk ripper. You've found one of the examples where the "patch to rip" doesn't work.
There are tools out there that ARE intended to rip disks. MakeMVK is one, but it isn't the only one. Rip to MKV files and hand those over to handbrake for encoding.
It works well, and you can rip dozens of disks quickly, even if handbrake is going to take hours to encode them.