You will be placing greater headpressure on the pump potentially deminishing the output.The added pressure the deeper the intake tube goes in the tank, in my mind would actually increase the flow up the tube, but if you leave it at the same level in the tank, the only water weight advantage will be the extra weight the extra pipe volume will give on the outside. Your filter is useing gravity(siphon) to aid in moving the water and it is much easier to start flow with a deeper placed downtube as the water doesnt have to fight its own weight, as much, up the down the tube. The added weight/pressure of the deeper water pushing on the moving water going up the tube would, I think, make the water move easier.
The water will then seek its own level which will be the waterline in the tank and the pump is just ment to give that final push up and over.
Centrifugal pumps only push, they don't suck, at least not that much, so the added weight of the water in the return line will push against the pumps impeller, decreasing flow(increased head), but, the increase in the siphon pressure may overcome the added head. I don't know if just a few inches will change much...try it out. I think the only problem you'll have will be with the return.
Just my 2¢.