I do use Nginx in docker for (personal hobby) dockerized applications... but I didn't fully understand some of your reasons:

* AFAIK "docker exec NGINX_DOCKER nginx -s reload" works to 'hot reload' configurations

* You're right that "in place NGINX binary upgrade" won't work. The "bright side" of this problem is that the "NGINX container binary" is immutable and can be easily "rebooted" if any corruption occures (instead of having to reinstall everything). For hobby websites (including the condo mail server), the downtime is acceptable (not much traffic, not really 24/7, fast restart, few versions of NGINX every year...)

For me: having an isolated (dockerized) NGINX is easier to manage (like a dockerized mail server) because it limits the amount of processes "on bare linux with files everywhere" and make is easier to backup/replace/upgrade (just start a new docker with a new version). YMMV