For the purpose of IDN, there is only one charset: Unicode. Charset mixing shouldn’t be an issue when processing FQDNs. I don’t know the details of the certificate specs although I would assume the aliases will be written in Unicode and/or IDN in the issued certificate so charsets shouldn’t be (much of) a problem there.
I don’t think the other CAs enforce such a policy in such a manner. LE is going to check each non-IDN domain name against Google’s API of bad domains names so why can’t the same thing apply to IDN domains? LE is making a good faith effort to enforce the policy without resorting to overly restrictive limitations on what domains can be registered and which not.
If the matter is purely potential confusion of humans, LE could mark FQDNs with suspicious characters and execute extra checks against that API at regular intervals and stop the extra checks after a certain time limit if it doesn’t appear on that list (only checking when there are renewal requests from then on).