WHMCS needs to have a way to support a multi-tennant or multi-company setup. This would allow companies like mine, which have multiple identities to keep branding in tact while at the same time, consolidating all quoting, support, billing, etc. from a single system.
Having to manage 2 installations is a PITA because you then have to have a separate hosting account, SSL, etc. You can already brand the frontend using the template= syntax in the URL.