Actually all the intake ports are really transfer ports. We started calling the port opposite the Exhaust the Boost Port because it boosted the charge upward to create the loop. Our engines use this loop to efficiently charge the cylinder and then empty the cylinder after the burn out the exhaust port. The side transfers are mass input ports to supply a LOT of charge. Opening the boost port a few degrees earlier starts the loop in a really straight line and CATCH the charge that the side transfers supply a few degrees after the boost starts supplying. Just a boost port wouldn't be enough to charge the cylinder totally so we need the area supplied by the side transfers.
I haven't worked a lot with grinding the channel that the side transfers use to charge the combustion chamber, but I suspect that it would make some difference in where the charge ends up to help it by some redirection. Of all the people that modify engines and work in that area, Stan, Jr and his Dad are probably at the leading edge of that technology. Jack and Steve O'Donnell probably know a substantial amount in this area as Jack has Teather Cars running over 200 mph and turning amazing rpm's.
Most of us RC boaters are more of the "Hacker Type". I am one of those
If you have ever seen one of Stan's liners, you would be amazed at the Jewelry Quality channels, etc that he puts in his parts.
There are some others on this Forum that are the real craftsmen in this area, but we seldom hear from them. Jeff Lutz is also one of them, as is Andy Brown. Would be nice to hear from them.
Since I started running the Nova Rossi 21DD I have not has to do a lot of modification. The engines are so well engineered that the pipe selection and carb selection makes it a dominant engine. I have found only a mod to the head button, a larger carb and some other very minor mods are all that are necessary. In fact I have run the engine stok (still can't spell that) most of time I have had mine. I now am starting to experiment in some more mods and each time it seems to give me more performance. Unless you have your boat/prop combination optimized, I wouldn't suggest that you do much. Once you do, then it does makes sense.