I think you're missing the point old fruit!
These are civilian aircraft operated by civilian crews as charter aircraft in the same way as Monarch, air Seychelles and numerous others have flown MOD charter for the last umty ump years. I guess the advantage of the MOD having its own charter airline is the ability to plan long term rather than renegotiate contracts every few months, have guaranteed assets available even during the busy package holiday season, not to mention the advantages of having such an outfit embedded at the RAFs AT hub.
The reason for using civilians where possible on benign routes and military where required for the warlike stuff is pretty obvious. Civilans are cheaper than military folk. Sure, the RAF can, and did, do the Falklands airbridge, Calgary, Nairobi etc, but why would you? It's simply an extension of the principle of putting civvies in second line jobs that has been going on for years.
Intersting times.