I know there plenty of shallow tanks out there, but my first concern would be more with "fillage" than drainage. Concern being with such a shallow tank, it is easy to imagine under the right circumstances, a pile of...solids...growing right up to the toilet flush valve over the course of a couple of days, and then you are going to have to do something to break it up...
Other concern would be that when you have a black tank above the floor, you can keep it warm in cold temps. Below the floor, if you don't have some means of heating it, it might solidify in cold weather.
Final concern, on emptying the tank: your dump valve assembly is going to take up 4-5 inches as well. If you dump from the bottom of the tank, you will get the most complete emptying, but you will lose the dump valve assembly the first time you go over a speed bump. If you drain from the side, you will not be able to get that exit fitting flush with the bottom of the tank, so you will always have some volume of crud in the bottom of your tank.