make sure you attach a ball valve on all the drains/return to control flow & etc.
if not you might just end up draining your whole tank water on the floor lol
I would personally just leave the overflow, paint the back black so it dose not stick out and grab some powerheads to up the current right where you need it in order to keep junk suspended in the water to be filtered out.
So your just running a drain on the bottom of your tank with no overflow box or standpipe and using a ball valve to match the drain flow with your pump? You do realize if the power goes out or the pump dies that your entire tank is going to drain, unless of course your standing right there and close the valve. or are you using a closed loop type setup in which case that setup would be fine, however I've never seen an overflow used in this way.
I agree, paint the back of the tank black and you will hardly notice the overflow. If crud is settling on the bottom of the tank add some power heads to move it towards the overflow.