Yes, you can do that. I did in my wet/dry filter. Only thing that I found is there begins to be an accumulation of crap under the rock. I think eventually you will have to suck it outta there.
Also note it makes a lot more noise once you do this. The water ran down the balls before. Now you have that gap that sounds like your in a urinal 24/7. Mine does not look like this anymore. I removed that blue tray. Put an piece of PVC on the bottom of each input that goes down to the water. I wrapped a filter sock around each PVC to catch crap. No noise!
See