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I didn't plan it that way. I installed Mastodon first and didn't use a Docker install. I configured Nginx and reverse proxy and then tried a non-Docker Lemmy install from scratch. That failed, and I believe the reason was some minor version differences in the dependencies. That's when I asked for advice and got a few recommendations to try the Lemmy Easy Deployment script. I would prefer to have done the from scratch install if there was current documentation and dependencies were available, but if there is I wasn't finding it. The Docker compose Lemmy install method worked well enough though so I'm happy with that.
Ah, I know what you mean. I managed to get them both setup in docker containers on the same server, but I'll admit getting Lemmy up was a pain. The documentation is vague on some steps, but it's FOSS so I can't complain.
Hope this helps!