This seems like a common feature request. Many people suffer from the fact that upon flush, the contents of single-file mailboxes are written into a new file which is then renamed over the old file.

For example: #1599254, #5346, #7359, #7360, #9559, 

The original design rationale was probably to prepare for crashes. When changes are made like this, a power loss, other sytem crash, or even a bug in the mailbox.py code in the middle of writing the mailbox, cannot destroy all the data in the mailbox file.

We could add a flag to the constructors of all single-file mailboxes that changes this behavior to in-place rewriting. This would of course need accompanying documentation that warns about that the same safety guarantees don't apply with this flag.