Why would this be such a bad thing, most in-sump skimmers are designed to dump back into the same chamber they pull from? The goal is to eventually skim the whole watercolumn, the only thing you might lose is some skimming efficiency, but what is gained is 1 less issue when your return pump shuts off and you are now draining the stable leveled skimmer section of the sump into the return chamber, potentially exposing any items in that section to air (like heaters/probes) and eventually running the skimmer pump dry as well.
Think about it.
If the output of the skimmer is dumping back into the same chamber/area that the skimmer input is pulling from, you are just recirculating the same, already skimmed water. Granted you will be pulling in some new water, but not as much as if the skimmer output went into the next chamber of the sump.
As for draining the chamber where the skimmer is, I doubt that, unless you have the divider all the way up to the top of the sump. Once the next chamber reaches the top of the divider, it will back flow into the skimmer chamber.
Try setting your skimmer up this way and see if you don't pull out more gunk. Also you can move your heaters etc to the second chamber if your worried about the water level droping too far.