In my case, I always use the domain name when creating site.
When I need to change the domain name (internet), I use the bash mv command to rename the site to the new domain name.
certbot --nginx lets you choose which domain you want to place a certificate.
For totally unrelated Companies with different application domains - meaning you expect to introduce custom apps, it is good to give each Company its own frappe-bench (bench init [domain-name]). You may install the apps (ERPNext and other custom apps) that the company would need.
This will allow you to customize individual companies without worrying how your customization may affect other companies.
Also, in case something goes wrong in one (renamed) frappe-bench directory, this issue will not affect other frappe-bench directories.
The disadvantage is, you have to do bench update on every frappe-bench directories.
But this could also be an advantage because you may have separate trial production frappe-bench directory where you test the bench update to check for issues, before you do the bench update command on production sites.