Yes your idea will work...
Personally I think the filter intake needs to be at the bottom of the tank where the waste settles. Having it at the top does help prevent oils from building up and disturbs the surface also... so ultimeately having both is 'best'.
If you took your idea of drilling the tank at the top (@ desired waterline) and mounted a T fitting on the inside of the tank where it's drilled... if you took one opening of the T and ran it straight down it could collect waste from the bottom... if you narrowed the other opening of the T to about half the diameter of the pipe running down, this would balance the flow between the two openings. You will not need to worry about the pipe at the bottom siphoning the tank empty because this line will not be a siphon. The benefit of a drilled tank is you can use an "overflow" instead of a siphon fed method.
If you dump water right on top of a sponge, naturally tons of waste will collect/pile where the water hits the sponge. If you are the type to clean media very frequently and not 'burn out' on such maintenance, that is fine. Personally I like the method of having water dump into a chamber, then water flow from that chamber through a sponge. This spreads the waste more evenly through the sponge allowing more time to go between cleanings without any ill effect (other than leaving waste in the system).