if the pipe that is used as an extension is larger than the OEM exhaust pipe, AND its not fully sealed at the joint, but lapped over the end of the OEM pipe about 6-8 inches and left unsealed, there is no need to worry about back pressure, as it will have a venturi effect as the exhaust exits the oem pipe... if it IS fully sealed (welded or band clamped, then one needs to take the back pressure into consideration....
as for routing, the exhaust pipe out of the generator can be unbolted from the muffler from below, and turned 90degress and bolted back in place. so the pipe points in a direction that can be adapted on to more conveniently..
I can see the desire to keep the CO to a minimum, and the smell if the genset burns rich, but on the last two onan generators ive owned, both 5500 marquis gold, the noise leaving the exhaust pipe was very minimal and could not even be heard over the sound that was exiting the bottom of the generator with the cooling air...