I've reproduced this and collected forkstat logs from installation of
snapd snap on an otherwise pristine "noble" system. I think what is
going on is that systemd stays in a mode where it knows that units on
disk have changed vs units in memory and will print the warning until
re-loaded. The fact that apt hooks fiddle with systemd units is
sufficient for printing the warning:

apt update causes this thing to execute:

10:37:56 exec     3523                 sh -c -- [ ! -e
/run/systemd/system ] || [ $(id -u) -ne 0 ] || systemctl start --no-
block apt-news.service esm-cache.service || true


This is enough for the warning.

The remaining question is where in the installation of snapd do we
modify units after last daemon-reload. I'm focusing on that aspect now.

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https://bugs.launchpad.net/bugs/2055239

Title:
  Warning: The unit file, source configuration file or drop-ins of {apt-
  news,esm-cache}.service changed on disk. Run 'systemctl daemon-reload'
  to reload units.

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