A highly customized Config.pro file can be confusing to manage and can become cluttered with duplicate entries - for both mapkeys and options. An option to specify a separate mapkey file would make managing these files much easier.
This is even more important since the ability to have multiple sessions has been added. This would enable using different config.pro files for different sessions and easily use the same mapkeys.
Regardless of the many possible post-installation work-arounds, this out-of-box solution would save a lot of (especially first time) users a lot of headaches.