I don't see the reason for this. Frankly I don't find deserts weak, at all. The only luxuries they can roll are mines, marble, and incense (which is awesome when it pops up on floodplains) all of which are very strong. I'm guaranteed a river system where all the tiles start at 3 food, that matches or beats what some luxuries do in plains or grassland. You get access to floodplain wheat and Oases, two of the best starting tiles in the game. Maybe I do have to work an iron mine or oil well that earns 2 food less than it would on grassland, but I'm earning at least 2 extra food from having floodplains, and that comes into play much later.
I completely agree with your bolded statement, but keep in mind you can have a mine on a hill without freshwater, and flat desert which is fresh water via Oasis. "+2 faith and +2 gold on desert tiles with improved resources. Additional +2 food if the tile isn't hills or floodplain" is the wording I suggested in another thread, I think it achieves the goal of making inhabitable desert habitable.