Hi Firestarter,
On the other hand, you can have the hole drilled higher up on the 3rd chamber. My off-the-shelf IOS tank has it this way. I mount my return pump on the hole to :
(1) Minimize heat release into the water
(2) Minimize pipes (just have a short flexible hose connecting from pump to bottom of 3rd chamber)
Have been running it this way for a year.
Cheers