I see some parallels with my own AIO setup, especially because this is also a Docker Compose based AIO deployment behind a reverse proxy with APACHE_PORT set manually.
I documented my own Proxmox + Nginx Proxy Manager + Nextcloud AIO deployment here, maybe it can help you compare the setup:
One important thing from my personal experience: the first AIO initialization can easily take 15–25 minutes depending on the connection speed and server performance. Some of the AIO images are quite large, so the initial pull/start phase may look like nothing is happening for a while.
In my own setup I usually prefer using Portainer for this part. It allows me not only to check the logs more comfortably, but also to immediately inspect and manage the containers if needed. During the first deployment the containers do not necessarily appear all at once — some are pulled and started later in the sequence.
So I would first check directly in Portainer whether the missing AIO containers are only still being pulled/created, or whether the process has actually stopped.
If the core AIO containers are not being pulled or created at all, I would also test whether the server can pull the core image manually.
If that fails, the issue is probably not nginx or domain validation, but rather Docker/GHCR/network/storage access.
Since this is a reverse proxy setup, I would also compare the compose file against the official AIO reverse proxy documentation and make sure APACHE_PORT and APACHE_IP_BINDING match the way nginx connects to the Apache container.