This used to be available in previous versions on WHMCS. I got this response from support when asking about it:
"As part of the Domain Checker refactor, this functionality was updated.
Subdomains are not considered valid when selecting "I will use my own domain"."
This was useful to our clients. The way it was used was putting everything before the first dot from the left in the `sld` field and the whole rest in the `tld` field.