Thanks, I'd probably try it in a VM first. I'm not incredibly confident it will work since it would have to know that when Server is installed on OS X the apache files are actually located in: /Library/Server/Web/Config/apache2 and sites within apache2 directory there.
Server.app assumes a bit of control over these and has it's own GUI cert mechanism and GUI for the websites. In looking around, I found some info right here in between replies on the topic and automating the import of the certs to Server.app:
I may give that a whirl, I admit while I can handle it, it'd be nice for a production/home server to have a lot of this rolled in to certbot itself. That's just a wish on my part, of course. 
Thank you both for the quick replies and info!