My experience is that the 2 cylinders are louder but more user friendly, since the power band is flatter. They will pull their load at lower RPM than the 3 cylinder engines. I think they are all too loud, and always wear hearing protection. The 2 cylinders make a lot of noise from the engine. A better muffler wouldn't really help. The 3 cylinders are smoother, and the sound is attenuated better. Additional muffling might dampen the sound even more.
Fuel economy is excellent for either type, with an insignificant edge to the twin cylinder. There really isn't much to choose as fuel consumption goes. All of them impress me, especially every time I run my 17 hp gas engine riding mower.
For reference, I have 14 and 15 PTO horsepower rated versions of the 3T72 in my 1401D and 186D respectively, and the twins are all some 2TR20 variant. My 186D is fortunate to have Powershift. It is very heavily ballasted, and really benefits from the ability to start off in first gear and shift up up and down to keep the RPM in the working range. My YM240 with a loader weighs the same or more, but will start in any gear from idle, and clank away happily. The 186D has no hope of doing that, and needs to be above about 2000 RPM to do much good, but the transmission lets it stay there. My 1401D has a loader but is quite light, compared to the 186D, and the power is much more tractable. I always run out of traction before power with that machine.
I don't advocate lugging the engines, and the 186D shows excellent fuel economy, so isn't suffering from being revved up, but the big two cylinders are very affable and friendly to deal with.
Others may have different thoughts or experiences.