There's two issues, timing and restriction of the secondaries. Timing has been retarded in the lower gears since the first R3's came out. The idea developed by riders is that this was done to restrict power. I'm skeptical. Correct timing is necessary for efficient combustion. Timing needs to be retarded at slower engine speed. I don't see why Triumph would choose timing to restrict power when it can easily be restricted with fueling. I would only be convinced by dyno runs in 1st or 2nd on any R3 done with both the advanced and retarded timing tables in those gears. On the other hand, Wayne MacDonald who invented Tuneboy did the first custom tunes for the R3 for Staintune and tor exhausts. He copied the high gear ignition tables into the lower gear tables. He knows what he's doing. However, the big difference in his custom tunes for the aftermarket exhausts was in the fueling. He also made a tune for triple filters and tors where he got the best power by retarding the timing in certain places. Wayne Tripp has said that unless you're a serious tuner, like him, you shouldn't mess with the timing. I agree.
As for secondaries, let's say you set them to be open 100% in every gear. When the bike is in neutral, they close. When you put it in gear, they open. So there's no lag in response. Besides, if you're racing, you would dump it at at least 3000 rpm where the peak torque is. My concern with taking them out is that at idle, the plates close. If you take them out, would it affect the idle? Since a lot of people have removed them with no apparent ill affects on the idle, the answer seems to be no. I've seen arguments that leaving the bar that the plates screw to would mess up the flow. Again, I'd like to see whether this or having the vertical plates in there has a measurable effect on power, as shown in a dyno test.