Sorry for late reply, was on leave last week
Not sure about the mechanism behind the .ALC file creation when dropping a Midi Clip onto Live's browser, I won't see that as saving a minimal project version though, it's more a channel strip with Midi Notes & device + effects chain save.
My guess is that since Midi Preset Change is not implemented in ANA 2, the .ALC file created that way by Live
will mess up your preset settings, not sure maybe @phil_johnston could tell more about this.
Again, though I know it's more convenient for faster workflow to just save a Live Project without the need to save VST presets first, it's not a 100% safe method IMO. Once you're done with your sound design it's worth taking the habit to use ANA 2 "Save as" feature from the GUI & save it into your user presets. It's the safest way to recall a preset in case of troubles.