(Another) Zelda Ripping Project!

[Alvare]

You have to manually separate the CMB from a ZSI file. Which is tedious.

...I don't find this frustrating or tedious at all. It is a common thing that each tool has it's advantage or drawback compared to one another.
The tools aren't build to be compatible with Majora's Mask to begin with, safe for N3DSCmbViewer.
Which was ultimately just meant to be used for extracting the archive and viewing the model.

Sure, having to hex-edit a header out of a file is time consuming, but easily done in a matter of seconds.
You skipped over Zar importer from Meltyplayer. https://github.com/MeltyPlayer/OoT3D-Importer. Which gets all actors and animations.
But, it has bone orientation problems due to Blender not doing it's calculations correctly. (Blender is kinda doing it's own thing with bone placement.)
You also skipped over the need to extract each actor's zsi archive to get the cmab file for mouths and eyes.

(Fin Model Utility) Works with OoT3D, but I can't get it to work with MM3D at all.

Well, if you looked and read the main page of the depository, you'd see the supported formats.

(Fin Model Utility) If something goes wrong in the middle of the process, no way to pick up where you left off. You have to run the whole process again.

That's a false statement.  When going through each zar actor, it can throw a detailed error and simply moves onto the next one in the list.

(N3DSCmbViewer) No options for other exports, or even just to extract CMB from ZSI files.

That's incorrect. You can click on Archive|Extract All to get everything instead of just converting to dae. This only works for .zar and .gar.lzs files with actors though.

(CMB Importer) Extracted texture files don't have ".png" extensions, which is a slight annoyance to work with.

Uhmm...? It does extract them correctly with png extension. There is however one particular instance in which if when an texture file shares the same name of the previous, the tool will put numbers behind the extension instead of behind the name. And that causes the extension to become unknown. But that's easily fixed with bulk_rename_utility or doing these few instances by hand.