1.0.4.6x versions included updates to support the extended security model for DB. At the time of release (of DB website) it was necessary to get the software from there because it was not on VG.
It was simple, you got new stuff and you needed a newer player to access it. This happens from time to time on VG as well!
Now that VG is also 1.0.4.65 I suspect that technically you do not need to install DB at all (provided that you got 1.0.4.65 from VG). Either way, you really only need one of the two pieces of software (as far as I can see) and the only benefit of installing both is to get the software specific skins. With the skins also come the weblinks to the associated sites.
For example, on my second machines, never installed anything from DB! 1.0.4.65 and I can play DB shows. It might be that the download or the install sets a flag on your account on the server.
So I am agreeing, looks like something could be made easier. But disagreeing in that a shared program and shared model/data folders works well (IMHO).