I'm not really talking about displacement, but rather, engine configuration. The best way to look at it is "all else equal". If just want/like more displacement, then a larger three-cylinder would be smoother than the same displacement four-cylinder and capable of the same power. It might be too wide or tall, however, so there may be a packaging disadvantage.
The smoothness is all about balance, reciprocating mass, and harmonics and there is a real fundamental difference in various engine configuration. If you're a car guy, you will know straight-six engines and V-12 engines are legendary for their smoothness, and it's the same reason a three-cylinder is smoother than a four-cylinder. Which engine is chosen for a given application, and why, is often dictated by packaging.
Tractors are just like any other application, and as HP needs go up, the natural progression is to increase displacement up to some practical limit, and then start adding cylinders beyond that limit. There are quite a few examples of this in Kubota's lineup, and some oddities too. The previous generation B series had three-cylinder engines in the
B2320,2620,2920, displacing 61.1, 68.5, and 77.0 cubic inches respectively, with a 2800rpm power rating, while the larger
B3200/3300SU had a four-cylinder of 91.5 cubic inches rated at 2700rpm. At the same time, the larger L-series 3200/3800 models had three-cylinder engines with 91.5 and 111.4 cubic inch displacement rated at 2700 and 2800 rpm, respectively.
So there is an interesting crossover, with a smaller
B3200 having a 91.5 cu.in four-cylinder (which was commonly noted to be a real buzzy engine, BTW) and the larger
L3200 having a 91.5 cu.in three-cylinder engine. Why would that be? Most certainly, it was because the B didn't have the space to squeeze in the wider and taller three-cylinder (lengthwise, the engines are within about an inch of each other). If it did, it would have gotten a smoother engine with the same displacement, rpm rating, horsepower, and torque. The L's 91.5 cu.in three-cylinder is known to be a stronger, smoother, better engine than the B's 91.5 cu.in four-cylinder (the three-cylinder also weighs more, at 148# compared to the four's 110#). This is a case where, all else equal, the B would have been better off with the three-cylinder if it could have fit. Or coming at it from the the other direction, it just wouldn't make sense for anyone to want the four-cylinder in the L -- the three-cylinder fits and is a better, smoother, heavier engine.
This is one example of many where you should not conclude that more cylinders are better, and it's the same reason I don't consider the
L4701's four-cylinder to be an advantage over three-cylinder engines as you claimed. If the
L4701 had enough space to accommodate a three-cylinder of the same displacement/power as its 148.5 cu.in 47HP four-cylinder engine, I think you'd find it was a smoother, better engine. But, once you start getting into that displacement range, three-cylinder engines would be quite wide/tall and not practical for packaging.