I like the skimmer Theo. What brand is it?
And, IF you are able to drill without breaking the cup, then, by all means - go for it (if you want to). The skimmer cup itself is just for collecting the skimmate. BUT, the most important bit is the inner bit of the "tapering neck". This allows the protein and bubbles to accumulate and form "foam". As long as you don't damage this bit... it should be ok.
Just to re-visit the sand-bed (if you don't mind Theo). The "thing" with the sand-bed:
Take into account the Joubert plenum design, then basically having a "rough and big particle" substrate at the bottom, makes sense, as this is basically just a different type of plenum. The main reasoning behind the small particle and substrate type, as far as I understood, is that it should be small enough not to clogg up like mud, and not sharp enough to hurt the tiny micro-critters that take up refuge and set up home, in the substrate.
Right?