Webhost that limits you this way are not competitive and dying fast. I would be surprised if you cannot find a more flexible web hosting firm at a lower cost. Which webhost are you with that still have such restriction?
I’m not using a such host, but I know it exist as I already encounter it and changed due to that restriction 
And it’s really low cost host.
After on my side we have our own servers, and we are deploying apps by subdirectories, but for several server names as we link a user auth on a domain it’s more easy to keep him on the good server name. But we can tune our servers and apps for a such case with some development for our customization needs, even if we prefer to avoid such cost.
For the server name management part I will follow your advice