The Debian package management tools are powerful enough to manage the whole system, but the Hildon Application Manager does not offer the full power to the user.
Instead, the Hildon Application Manager is intended to be fully compatible with existing and future interfaces to the package management tools. It should be possible to, for example, freely alternate between apt-get, synaptic and the Hildon Application Manager and not have anything break. Thus, if you need more power, you can use Debian package management tools directly, or use one of the more powerful interfaces.