The error message is related to the SSH library which was updated. IIRC, the default trusted algorithms are a bit stricter, which would explain the change in keys. I am not sure how the fingerprint is created, but the 16 bytes are returned from the SSH library (and server), and I think this is part of the key-file hash (including all lengths).
You can see the number after ssh-ed25519 is changed from 32 to 256, so what I understand from the error message is that you are seeing the same server key, but now using the 256 bit key instead of the previous 32 bit key.
I am not aware of any changes related to the temp folder.
I looked at the source and the intention of the --run-script-after option seems to be to delete the temp file immediately after the script exits.