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I will almost certainly be removing sandboxed Google Play Store, but keeping Google Play Services for now.
This is thoroughly broken, unsupported and doesn't make any sense. Your assumptions about what is happening are highly inaccurate. Nothing unexpected or problematic has happened. Aurora Store is a frontend to the Play Store and you're still using the Play Store with Aurora Store. It's clear what you think is being avoided by doing that.
Google Services Framework is no longer a stand alone app in GOS
It's obsolete and not needed anymore. No functionality was lost without it.
which from my recollection was the only thing necessary for Signal (and other apps) to use Google's battery-efficient Firebase Cloud Messaging (FCM) for notifications
No, this was never the case. FCM always required sandboxed Google Play Services. You can use UnifiedPush with a MollySocket server instead with Molly.
So in order to keep FCM capability I will apparently have to keep Google Play Services (GPS) installed. Hopefully GPS is not in any way connected to the privacy compromising issues I have experienced with sandboxed Google Play Store.
FCM never worked with only GSF which isn't useful anymore. None of what you're assuming and claiming happened with the Play Store actually happened. You're wrong and are spreading misinformation about GrapheneOS with no basis. Your posts are likely to mislead other people.
If I decide to stick with GPS, even though Google has my main profile fully fingerprinted now since I installed it on my primary profile and I use my primary profile for just about everything, it still may be wise for me to uninstall both Play Store and Play Services and then reinstall only Play Services so Play Services is not directly tied to my Google username/account. Whether or not this will help to mitigate any privacy issues, I don't know.
Your claims about what has happened as wrong. Choosing to sign into an existing account instead of making a new one was entirely your choice and not in any way a problem with sandboxed Google Play.
Lastly, I will say I was extremely happy with sandboxed Google Play Store in the past (I have used it since it was introduced a few years ago), but with since latest experience, I would have never installed it if I had known the issues I would have encountered ahead of time. As Google becomes increasingly authoritarian in its policies (perhaps they are even specifically trying to sabotage GOS's sandboxed Play?), hopefully more developers will begin offering their apps on secure and privacy-respecting Accrescent.
Everything you've described which actually occurred is an expected result of what you were doing with it. Your assumptions and claims about what it must mean are highly inaccurate. Nothing about sandboxed Google Play has been sabotaged and the claim doesn't make any sense. It is working as it's supposed to work. You're making wild interpretations of what's happening on your device because you have a conclusion you came to and you're looking for evidence for it. What you think you've found as evidence for what you think happened is not and none of it indicates anything wrong or unexpected. You signed into an existing account so of course it's signed into an existing account because you chose to do it and did it. None of this means anything is being tracked in Vanadium, that anything was done without your permission in violation of the OS sandbox or anything else like that. None of that has happened.