As long as you do not alter the intake or exhaust timing on a two stroke engine and do not alter the squish band or combustion chamber design, then the idle / transition properties will more than likely not be affected too much, if at all.
I have modified many engines in the past without altering the stock timing and have had some results better than others. A lot of it depends on where in the rpm band you intend to do most of your flying. So, smoothing out and opening up a lot of ports in an engine that is used mostly from off idle to mid throttle will have a lot less (if any at all) affect on power to the prop in the low throttle settings where the intake velocity is not very high. If you are flying at high throttle settings most of the time like in combat, then the extra few hundred rpms will be noticable.

Everything like Dar has pointed out will no doubt eliminate all factory warranties.

I think that the modification is popular on car engines because many manufacturers either do not warranty engines or limit warranties to 30 days.