One of the main driving factors to how a component is made and is available to the masses, is what the masses want to see. As of right now, there are enough SFF cases that cater to large or long or girthy GPU's/components. So if a market survey reveals that smaller cards are but a niche area of the market there are less resources allocated to said SFF cards.
The other aspect is that the sort of heat output on GPU's. If you want to tame the heat on hot headed cards then you will need to amp up the cooling with better quality fans or exotic materials on the cooling assembly which will in turn drive up the costs of said card, so if the card is too expensive, you might be driven away from it to buy a regular GPU.