Earlier quoted context omitted.
It's not easy but iirc you can do it with a DNS-01 challenge, if your internal domain name is valid (doesn't have to resolve to anything though).
The problem is that I also have domains which are completely internal, not known/resolvable outside
Realistically you can't entirely deconflict these names. So you always have a risk of shadowing names from the public Internet.
The public CAs spent years in denial over this (yes they used to sell publicly trusted certs for "private" names, this is now prohibited). Create internal.example.com and things get easier. To the extent security by obscurity is worth trying it's just as available this way (split horizon DNS etcetera)