WHMCS Provisioning vs Domain Mapping

WHMCS Provisioning works wonderfully with mapping domains automatically when creating new sites with domains. I have a problem when creating simple subdirectory site on the same network. For some reason the newly created site have assigned domain althou it shouldn´t be domain mapped at all. I believe it wouldn´t be a problem with a subdomains, as it is mapped as subdomain (clientchoise.domain.com)however I use subdirectory and it should be domain.com/clientchoise.
What happens now is that all page previews and all links from admin area generally are pointing to subdomain and, as it does not exist, it does not work.
From what I understand now, WHMCS Provisioning puts both domains and subdomains in the same bucket. Wouldn´t it be possible to skip applying subdomain/subdirectory to map it self as that actually does not make sense anyways with a little php magick or something?