ok, here is an idea. make the base of the skimmer into a sump of sorts. this is basically what the big name skimmers with the box bottom does. this box bottom a 12" box would be plenty big enough for this. it will also give the skimmer a good base to stand on. the base of the skimmer design would need to be a bit different, but nothing to bad. that way the base water level will not be a problem. it will also keep the bubbles even more in check.
the biggest problem i can see with this is maintenance. in order for you to take the skimmer way you would need to do a double union somewhere to keep the water at bay. this can be quite expensive if you are using 2" fittings.
prolly the best thing to do is raise the skimmer up above the water level in the sump. that way if you needed to work on the skimmer just turning it off would drain it completely for easy removal.
hopefully all of that just made sense.
G~