The validation reports
Home directory : Home directory /home/username/domains/alias.com does not exist for an alias domain which should not have home directory. Disabling and re-enabling the
Apache website enabled? doesn't help. Only removing and re-creating the alias virtual server makes the validation error go away, which requires additional hassle.
I believe Virtualmin validation should not be complaining about absence of home directory for an alias virtual servers in the first place, hence reporting this issue.