Sorry if I misunderstood you but are you saying that a 2 into 2 witch each a different frequency would be better than a 2 into 1 with one muffler on the right frequency ?

Do you know of any good sources to read about this ? Online or in book form

Some Aprillia bikes have a 2 into 1 system where the single muffler is tuned to two different frequencies to give a broader torque band. So, I'm not sure what you mean by the "right" frequency since it's always a trade off on muffler length and pipe diameter for the reverse wave back up the pipe. I'm not even sure how much this matters after the collector.

A 2 into 2 system, as defined by the videos, is where each cylinder has it's own exhaust pipe and muffler and there is no cross over pipe between the two. This type of system gives a torque and hp peak with a dip at a lower engine speed, as explained in the video. I'd prefer the 2 into 1 system with the nice broad torque curve, but the 2 into 2 system could be better for racing where peak hp is everything.

I don't know about any books, sorry. I'm not an expert either.