I'd suspect that the Originating Machine items would be relevant: "DESKTOP-7E9VL2T" corresponds to one OS installation, while "ilLUSIon-pc81" corresponds to another?
That does seem to go with the supposition that I'd made that these Restore Points are indeed all in the System Volume Information folder for the drive, mixed together in a way; whether that provides information that would be suitable in classifying these Restore Points... possibly, but that goes beyond my expertise, I fear. I will leave that to our development team to consider further. :)
Though, you do mention that the installations are on different partitions - each partition should, so far as I'm aware, have its own System Volume Information folder that should prevent such 'crosstalk', so that only puzzles me further.
(Thanks, Hazel, for digging up the PowerShell instructions for managing Restore Points - wasn't aware of that either, though I suppose I really ought to have!)
With that in mind, I do need to say that System Restore is a Windows process - therefore, the absolute safest possible means by which to manage it would be the tools built into Windows, so if that is your concern, then I would suggest using the Windows System Restore tool itself to manage the Restore Points; that does mean you'd need to do in each installation of Windows, of course.
Also, just to clarify, the Restore Point deletion feature is not a new feature - it was introduced in v2.19.901 in May of 2009 (only supporting Vista and XP at that point); we don't have any plan of removing it, though, so no worries there. :)
With that in mind, I do not believe it is optimized for your specific use case. It's intended for a user with a single OS installed to manage the Restore Points associated with that OS, as that represents the overwhelming majority of our users.
As an aside, System Restore itself is also meant to be simple, 'first line of repair' option for users that otherwise just stays out of their way and doesn't need management; I suspect this is why the tools built into Windows are fairly minimal, and why so few third-party programs interact with it. (CCleaner is also the only one I'm personally aware of; I'm sure there must be others out there, I've just not had the opportunity to look for them.)
For the sorts of needs you're suggesting, I think I'd second Andavari's suggestion of making 'known good' disk images periodically, as that will tend to be a more reliable and robust way of repairing your system - I've seen System Restore outright fail too many times to want to rely on it, truthfully.