I use Melodyne in ARA mode in Cubase Pro (currently 14.0.32, but going back to whichever was the first version of Cubase Pro that supported Melodyne via ARA – maybe 10.5???), and it generally works well. I’ve never even tried it via the VST3 plugin version. I’m on Windows 10 at present (move to Windows 11 coming “soon” – waiting for hardware components for a new PC build to arrive at the moment) if that matters. I also use Melodyne Studio 5 (whatever the latest version of that is).
With respect to your specific notes:
On #1: I think I’ve had the no sound on moving blobs thing happen occasionally, and I generally haven’t figured out when it does and doesn’t. I know there is a preference-type toggle in Melodyne that changes the behavior, so maybe I’ve accidentally hit whatever shortcut key changes the status (I know I’ve had that issue in Cubase in other areas, too, especially in cases where I meant to use a key shifted or unshifted and accidentally did the reverse due to whatever I was doing before that). But I’m more likely to use the visuals than the audio feedback while moving notes, checking my results with playback, so I haven’t really tried looking deeply into what is going on.
On #2: I wouldn’t see this as I do my comping first (and then fade editing and bouncing that fade editing to get the audio solid) prior to tuning. I think I might have tried something with another ARA plugin with lanes at one point, and it just seemed to be too confusing.
On #3: I am using this across multiple tracks (one part per track), for example when working on tuning background vocals or lead vocal doubles. (I’ve always tuned the lead vocal first, then time-aligned the doubles and any BGVs that needed that with VocAlign prior to tuning BGVs.) Melodyne is pretty flexible on this. You can have individual tracks not show up at all (nothing checked in the overview), tracks show up for reference only (silver/gray choice checked in the overview), and/or tracks able to be operated on (orange/red choice checked in the overview). If I’ve got a lead vocal in the picture at this point, it is for reference only (I’d already have tuned that separately, often prior to even tracking BGVs), so silver. I may sometimes tune multiple BGVs at the same time (orange) in simple cases, but, if things are tricky, I’ll keep all except the one I’m working on in reference mode (silver) while working on a single part (orange). What gets in Melodyne at first depends on how you’re using it in ARA mode. If you are using it as a track extension (i.e adding it in the track header), it will be all audio clips in the track. If you do it by selecting clips (potentially across multiple tracks) and adding the extension there (e.g. right click/Extensions/Melodyne), then it will be all those clips, but not the other clips on the same track – unless you already have the Melodyne extension active on those other clips, in which case they will also show up in Melodyne ARA. (My general M.O. on this is to operate on all BGVs for a song section at a time, then bounce the changes to audio before moving on to the next song section. I’ve only tried the track-level ARA extensions a few times and found them more confusing.)
On #4: I’ve definitely had ARA extensions crash Cubase at times – I know for certain I saw that with WaveLab 12 ARA (I think on trying to make the extension changes permanent), and I’ve probably seen it occasionally with VocAlign and RePitch. I can’t go so far as to say I’ve never seen it with Melodyne, but, if so, it was probably a long time ago. In general, Melodyne ARA has been pretty rock solid for me.
Your notes in general make me wonder if there is something in the workflow you’re using that makes things way more complicated than the way I generally use Melodyne (and ARA plugins in general). For example, as mentioned above, I really don’t use ARA extensions while I’m still comping. And, after finishing the comps, each part ends up on its own track, and I do the clip fade-type editing at that point, before doing further editing like tightening and tuning (except that if there were any very high-level tightening needed, such as moving clips around, I’d likely have done that in the fade editing). I do back up the earlier iterations of tracks (e.g. pre-comp, comped but pre-fade editing, etc.) along the way, just in case of needs to change my mind somewhere down the line, but, otherwise, I am treating these operations as destructive editing. Also, it would be extremely rare for me to leave an ARA plugin active in a saved project – this was a lesson I learned back when I was using Melodyne in SONAR at a point where there could be instability with the saved ARA extensions that could prevent loading the file, though it may no longer be a problem (and conceivably never was a problem in Cubase).