Well, what’s are your reason for using paid SSL cert? From mine point of view it’s unnecessary burning of money, make yourself a favor buy i don’t know,… S&P500 instead,…
Anyway, Mailcow is usually setup to use only one FDQN while it’s communicating whit outside world, that is the one you can find in mailcow.conf under MAILCOW_HOSTNAME that is the one docs you linked want you to install.
If you want use another SSL cert, for let’s say separate access to webmail, I would suggest to use reverse proxy before Mailcow and set up your secondary cert there.