Comment # 1 on bug 1140472 from Ignaz Forster

This is referring to
https://www.kernel.org/doc/Documentation/filesystems/overlayfs.txt, section
"Changes to underlying filesystems": "Changes to the underlying filesystems
while part of a mounted overlay filesystem are not allowed.  If the underlying
filesystem is changed, the behavior of the overlay is undefined, though it will
not result in a crash or deadlock."

Practice shows that changes done to the currently active system will usually
not be visible to the update environment, but there's no guarantee. In the
worst case it may happen that files from the live system that were changed
after snapshot creation could be visible during an update already. It should be
added that those files would be visible on next boot anyway, but it may
influence e.g. scripts that don't expect the different contents. (Example: A
package gets a major version update with a new configuration file; after
package installation a script tries to customize some values; while the package
was installing the same configuration file was changed in the live environment;
if the file leaked into the update environment the customization script may
operate on the wrong version of the configuration file.)

Unfortunately there is currently no way to formalize the behavior. My original
thought to use overlay snapshots
(https://github.com/amir73il/overlayfs/wiki/Snapshots-HOWTO) also won't work,
as those have the same limitation.