Derek if you run the water level higher, then more foam spills over into the collection cup faster. This will cause the collected foam to be less nutrient rich, and this the skimmer less functional.
If you shorten the neck, then the water level has to be lowered to get the same foam consistancy (or the exact problem above will happen). This again will decrease the output of the skimmer by in essence making it shorter with less contact time.
The only thing you could do would be to lengthen the skimmer body and shorten the neck. This will allow the water level to be dropped to compensate for the shorter neck. The skimmer body is taller, so the skimmer is again as (or more) efficient.
Also from my meager experience, a slightly dirty neck seems to produce better skimmate than a freshly cleaned one. This may just be my own biased observation that has no truth in reality.
Bean