First I’ll just expand slightly (for clarity of others who may read this thread as well). There are two different things here. The Certificate Authority (Let’s Encrypt ) and whatever client you use to get the certificates from Let’s Encrypt - certbot being the official client and many alternative clients.
So in answer to your initial question - does the CA (Let’s Encrypt) support what you want to do - yes.
In your subsequent question of how? then it depends which of the many clients is best suited to your requirement. Certbot requires the apache config in separate virtualhosts if you want to do it automatically from there. Other clients are slightly different, and could potentially read from your virttualhost.map. With limited information about your setup though, it’s tricky to give detailed, accurate advice.