You've misunderstood.
Something must be wrong with my setup then. Libreelec with kodi and home assistant in a docker runs fine and smooth. When I restart libreelec, the HA docker (which I installed using command line) does not get destroyed and recreated.
Nginx letsencrypt and duck dns gets destroyed and recreated.
Docker addons are not the same as docker containers you manually create. Addons use systemd to manage the containers in an automated fashion. The destroy/create is part of the automation. It is perfectly fine as docker containers are ephemeral by design. It is how docker is meant to be used. If you ever want to update the homeassistant container you manually created, you will have to destroy and recreate it based on an updated image (manually). Addons do that automatically without user intervention.
The validation is performed when the container is started for the first time. Nginx won't be up until ssl certs are successfully generated.
"started for the first time" refers to starting it with no existing persistent data. The persistent data (including the certs) reside in the userdata addon_data folder by default. As long as it's there, certs are not regenerated until they get close to expiration.
In any case, it sounds like this is a case of the xy problem. Let's focus on the boot delay. I assure you I'm running plenty of docker addons here on an rpi4 with no noticeable delay. The only delay I'm observing is "waiting for network" before kodi starts.
Check the kodi log to see what's holding things up during boot. Also check the addon logs with journalctl -u docker.linuxserver.letsencrypt and journalctl -u docker.linuxserver.duckdns (you can also try journalctl -u docker.linuxserver.updater).
With that said, make sure you update your addons and refresh the repos. There was a brief period of time where the addon updater caused a boot delay of about 10 minutes due to a bug in its systemd config. It was fixed shortly after.
EDIT: As a test, I set up all three containers in question, two as addons and one manually. I even created homeassistant with the same docker run from your other thread, all on an rpi4 with le 9.2.3 and I experience no boot delay at all.