When signing up for mastohost with an existing domain I own (whatever.com) the signup process forced me to use a subdomain (something.whatever.com). I don’t currently have a website on that root domain, but I would like to one day. Do I really have to have a long three part domain? Is there a way around it or is this a limitation of mastodon/mastohost?
The message you posted seems to indicate you can’t use “whatever.com” if there is another site already there, because of course you can’t… the same name can’t point two different places (well, it technically can, but don’t do that). I’m not super familiar with Mastodon, but this sounds like a warning rather than a restriction.
In any case, yes, you can make whatever.com a DNS alias for mastodon.whatever.com and handle it with configuration. Just be aware that if you ever want something else at whatever.com, it’s not easy to change the name later.