You are right, the drains are to silence bubbles. You can't see it in the pics, but I have overflow holes drilled in to the top of the first baffle. If/when the filter socks clog, water will flow into the bio area.
I based this setup on the Aqueon Pro-Flex sump. My 90 has a 36x18 footprint, so I don't have much room under the cabinet. I'm trying to go for as much bi- filtration (5gal of bioballs here) as my space will allow and stay on a budget.