To do that, I wish to store a copy of all the files the app has written to my filesystem, and put that copy outside the app's control. This is explicitly to contain data the app's developer does not WANT me to be able to keep.
A. Is my being unable to do this "more secure"? If so, why is the specific threat I described to my data integrity - an app developer deleting my data - invalid?
B. Does GrapheneOS support this protection, ensuring the device owner is secure against the app developer, or do they instead secure the app developer against the user?
Also you are misrepresenting the threat model. The problem is not an app deleting it's own legitimate data.
P.S. On GrapheneOS you can block apps from getting Internet access to limit their bad ideas.
I want to install an app now, and protect against its developer doing a rugpull on my local files later. I do not want to need to review each new app version in advance as I install it.
This is clearly a legitimate case where what the Android security model says I should be permitted to do makes me less secure against an attack by the app developer.
Also your argument about a user inspecting and editing application files feels like a strawman argument. For example many spyware use malicious links to infect the devices, not malicious apps.