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I can see this working if checksums are calculated per-item instead of as a group.

They are calculated both ways.

But if an OEM does this to a lot of apps, that adds up and it's a lot of disk space the customer paid for, purchased, and cannot use.

I apologize for being blunt, but yours seems like a very lame technical excuse to justify existing behavior, at cost to customer experience. They could just as well put it somewhere where it's (1) still signed and (2) doesn't affect the signature of the base OS.

And even ignoring any potential checksum issues, uninstalling that kind of apps consequently only frees up space on the system partition, where it is of little value to the average user.