ya, 2 1/2 inches doesn't sound like a lot of room at all! Not sure how you would get any skimmer in there, unless you got it in, then moved the 50g sump in place and then just kept the skimmer in there forever!
Not a recommended plan btw as you will inevitably want/need to clean out the skimmer. Then there's the issue of cleaning out the skimmer's collection cup!
You will save yourself the agony by giving yourself more room to work with under there. There's lots of stuff that goes on in your sump that you'll be tinkering with forever!