I have a multisite setup using subdomains on the same dedicated cpanel server. Myself and my server providors are currently trying to work out what configuration is required for the WHMCS and if it is required to be on the primary domain. Penguin internet would normally reccomend to have the WHMCS completely standalone so there can be no issue of a compromised plugin from a different script making this vulnerable - they would normally recommend keeping this on a different domain to reduce potential issues as your WHMCS may contain payment information etc.
This multisite provisioning setup is not something they normally see requested. My primary domain has no premium plugins, with different subdomains used for seperate sites. I would have thought that it would need to be installed on the primary domain along with prosites for this multisite specific setup?