Yeah, I had lots of service configured like that, and you are correct that it is awesome, however I have other services on other hosts (not on docker swarm either) so I needed to delve into file config quite often, and doing some web dev work, I had services that weren't dockerized, so I ended up creating dummy services (socat containers) to make them easy. It just got a bit frustrating and taking too much headspace, I was able to setup caddy in about 2 hours one evening, so I am pretty happy so far, and I can see all my hosts in a single file which is great ( I ended up with orphaned routes etc.. from containers I forgot about when I was testing things).
As you say, different people come at the same problem and come away with totally different views ( which is pretty great that there are enough option that we can all find something that works for our needs ).
Are.you able to identify what dns provider youa re using, as I read the error as being related to the cert resolver not being able to access the correct zone from the DNS provider. I am using cloudflare and the Caddy file looks pretty similar to mine, so I aren't sure the issue is there.
One other thing to try is to restarts caddy, I found that sometimes reloading my caddy file wasn't enough, and thing seemed to stay working after I restarted the docker image