One reason, is alot of the skiffs are butt heavy. The consoles could be mounted more forward. The 45/55 is somewhat farther forward.
All the folks hanging heavy 4 strokers on them aint helping either.
But there are other options as well. You can install the ball stoppers. Unless water is running out of the scupper, a ball is floated up to seal it off. You need to get the right size though and may actaully need to change the size of your scupper holes to work properly.
Another option, Drop a good sized bilge pump in the rear well if it has one and raise the scuppers an inch. The boat would self bail to an inch deep....which the PPI on a Carolina Skiff is going to be high so it'll carry an inch of water like no tomorrow. PPI is pounds per inch of immersion. A good sized flat bottom Carolina Skiff is probably around 500 pounds pounds.
That would be every 500 pounds the boat sits one inch lower in the water.
If I ever run across another one to restore, I'll raise the sole in it.