While that may sound like a good idea (not having the magic key 2/3 & pass-thru sticking out of the ds all the time), I personally don't think it's going to happen.
Right now, the developers are focused on exploiting the full capabilities of the magic key 2/3. Many functions (such as NDS saving) are imbedded on the magic key itself. I doubt they are even thinking about de-coupling the unit and developing a separate loader just for the flashcart.
At least the upcoming flashme/menu .7 will eliminate the flashcart requirement for booting.
The neomax software has a lot of potential, though, as a multi-boot app once it gets fully developed.
BruceG