A decent 2 into 1 for a road bike might be very difficult. With a race bike, the exhaust system can usually go under with no problem. Down the side usually ends up with unequal header pipe lengths. The exhaust system does more than just carry the gas away. If you think about it, you will realise the tail pipe resonates at twice the frequency of one of the header pipes, so if it's length is the same as one of the header pipes, the harmonics work out to be correct, However the if the tail pipe offers a restriction to flow, you lose more off the top of the usable rev range. For a road bike, a 2 into 1 with cable-operated Exup might be good. But you need to get it under the bike.
I had a 2 into 1 on my 500cc Triton - down the side, during a race my boot heated up, but because I was well up the field, I stuck with it and endured the pain. I got a second degree burn.
Getting performance without making more noise can be very difficult.
I looked at the Paul Dunstall 2 into 1 into 2 system. The 750SFC Laverda twin pipe system with the cross under the motor, might be better. Sound does not like going around corners. The Laverda has a 180 degree crank, so the pulses are not equal. It still seems to work. I have only ever seen one 750SFC racing. It was better than the Z1 Kawasakis in 1973.