Yes, you can have multiple instances of MakeMKV running simultaneously on one machine, each with control over one or more drives. In Preferences->IO, enable "Ask for single drive mode", and you will be asked which drives (default all) this instance should control. This will test your destination drive bandwidth; when my network was down to 100Mb/s (bad cable), it was hard pressed to keep up with one instance of MakeMKV. When that was fixed, I can run 3 at full speed, ripping BDs are up to 10x speed.
Handbrake is CPU intensive, MakeMKV is not. I regularly start handbrake on encoding as soon as I can set up the first job. It and MakeMKV are "harmonious" in that sense, because handbrake doesn't do a lot of I/O. If you have enough cores available, you could even run multiple handbrake instances (I don't have enough, but I have tested this) attacking different source files. (the handbrake team is working on automatically doing this right now, in their nightly builds)
Don't be discouraged from experimenting. I can see the value in "one step conversion", especially if you only want one thing off of a disk. It just isn't as practical once you have more than one disk, you're experimenting with different settings, or the disk isn't "perfect".
The other major problem comes when you do that next update on the operating system, and that integration breaks. The solution you list above should survive MOST of the things Apple has done to cross-program integration in the last 5 years, but there are no guarantees. Even though they do not recommend it, the handbrake team has a LOT of support requests for "why doesn't DVD reading work anymore?"
But there are a lot of things out there that are more "fun hacks" than "practical solutions". I haven't tried them all, yet, but...