The short answer is "yes"...the longer answer is..."it depends". Old aero joke...sorry.
Joking aside, many high performance techniques will transfer well to maximizing fuel economy. Not the particular solutions, mind you, but the techniques of, in this case, airflow management.
Racecars seeking downforce generally fall into one of two categories, flat-bottomed or tunneled. Flat-bottomed cars are just that. The underside of the car has to be built on one plane from side to side and front to rear except for specific exceptions, such as openings for the tires. Tunnel cars are permitted varying degrees of camber to their undersides. Both types of cars generate downforce by varying their ground height and "rake" (the difference in ground clearance between the front and rear). Both also seek to maximize downforce by employing side skirts whenever permitted to maintain nice linear flow under the car from front to rear.
Looking at the photos of basjoos' car, especially these two...
...it is clear to me that his car has considerable camber along its longitudinal axis. The leading edge of the nose appears to be about a foot off the ground. The bottom then dips down to within ~4" of the ground, and then gradually rises back up to the trailing edge of the car. In aero terms, basjoos has created a classic venturi, with a convergence zone at the front, a throat in the middle, and a diffuser at the rear. And since he writes that the car is stable up to 100 mph, my guess is that Aerocivic is producing modest net downforce. This added downforce comes at the cost an increase in induced drag. That said, the total induced drag on such a narrow-span "wing" (the car is only 5' wide or so) is slight. In other words, there is enough downforce to securely "plant" the car to the ground, but not enough to cost him much net fuel efficiency.
Basjoos, have you done any back-to-back fuel economy measurements with and without the side skirts? My guess is that they are giving you a measurable boost in FE. The question in my mind is whether you need both the inner and our skirts. I am fairly confident that if you remove the skirts and put boat tails behind the front tires that your fuel economy will suffer.
Be fun to find out, though!
Stan