Could just do like I do and make it lemmy.whatever.tld and mastodon.whatever.tld

I think subdirs would break the whole fedi handle system; deafboy@deafboy.social/masto wouldn't make sense to most clients.

yes you can use the same domain, but you may need different subdomains for everything to work happily.

It looks like there is a way to run Mastodon on subdomain.example.com, while having user ids in user@example.com format. https://github.com/felx/mastodon-documentation/blob/master/Running-Mastodon/Serving_a_different_domain.md

But since I have no idea how lemmy addresses users from other instances, this might not work for me.

By no means an expert but how do you want to set it up? Different subdomains or folders?

I think subdomains are actual FQDN’s and will not cause issues. Folders might be an interesting experiment.

How is that going to even work, technically?

I think you should try it out just to see what happens. Worst case it doesn’t work, and if it does work there’s a good chance you’ll uncover some bugs that need fixing.

Yes, but at least one of the services must be using a subdomain.