Part of the problem is that Debian package management, while wonderful, doesn't provide any facility for installations split across disks, where one of the disks may be removed or replaced at any time.
The idea is to have a core installation (including a desktop env, and some applications) installed on the (fast) built-in eMMC, and then a SD card full of DBP files.
DBPs will generally be user-facing games and applications, mostly dependant on common libs in the core installation, and will rarely(?) depend on each other.
The main reason to use DBPs instead of Debian packages is to save space and wear on the Pyra's internal memory. In the case of the Pandora, we only have 500MB internally - which is clearly not enough for a complete linux installation with hundreds of games.
Since DBPs are not (and cannot be) Debian packages, a different repo, and a different package manager are needed. That said, a DBP is a self-contained file, so most operations on them can be performed with your favourite file manager anyway.
Any native package manager for DBPs should support third-party repos, if anyone feels like hosting one.