I believe that's part of the reason to put a sand cap on the dirt - to slow the rate at which the water will circulate through it, and cut down on the amount of substances leaching into the water column from the dirt.
It's good for plants since they grow their roots into it, and can pick up whatever nutrients directly.
I don't think there is much need to use flourite either, if you have a cheaper alternative. Also, 3" of substrate will take up a lot of room in a 10gallon. You might want to put just a bare minimum of substrate in- enough to cover the bottom/look nice, but not to take up so much of the tank volume.
I don't think there is any problem with your plant selection, could be an interesting tank, but I think the setup can be a lot easier/simpler then what you are planning.
I know you weren't planning on putting any critters in, but it might be worth throwing even a couple feeder guppies in.