One thing you might need to watch out for is the length of the names themselves. Somebody many years ago decided the Common Name in a certificate subject would never need to be more than 64 characters. This wouldn’t be a problem except that for compatibility with software of pensionable age the Common Name is always one of the FQDNs your certificate is issued for.
If even one FQDN in the certificate is short enough, Let’s Encrypt can figure out how to issue. But if they’re all too long it gives up. So a.sub.sub.domain.example is fine but if the names are all like geraldine-simpson.my-internal-network.the-royal-company-of-haberdashers-and-cartoonists.example then you might be out of luck. There is a long term plan to fix this, but it won’t work with such names today