If there are no advantages of creating the index together with the maps
directly form .osm then maybe the mdr branch could be completely forked
out to be seperate from mkgmap?
    

There is no advantage apart from ease of use, however the same could be 
said of gmapsupp, tdbfile file, overview map etc all of which will work 
happily on the .img files.  The new code for mdr will also be useful to 
create a proper overview map too.

..Steve
  
Thanks for your answer. Better Overview map sound good, because it was not yet really correct.

Could you look into the issue that for big maps like germany.osm.bz2 index creation happens "there is not enough space in a single .osm img...."
Garmin City Navigator 2009 _mdr.img is 407MB big, so there are some limatations that are not needed for mdr.img