Normal sound. Here is why. The L3301 and L3901 are 3 cylinder engines. They fire a cylinder every 240 degrees of crankshaft rotation. In between firings, the crankshaft slows down a little. Then when a cylinder fires, the crankshaft speeds up. The crank is connected to the transmission, which runs the PTO. Every gear inside of the transmission has a little bit of clearance between their teeth. When the engine is running at lower speeds, the constant and regular fluctuation of the crankshaft speed causes the gears in the transmission to clash against each other which makes a little noise. If the PTO shaft had a little bit of load against it, say, bush hog or finish mower or whatever, you would not hear the noise as much because a more or less constant load is placed against the PTO geartrain.
The L3200DT's were really noisy, but it is normal. 3301 and 3901 DT's are also noisier than the HST's are. The HST places a more or less constant load on the engine which helps smooth it out a little, which also smooths the transmission/PTO a little as well. And sometimes this is an issue with dealer techs who are writing work orders; a customer might bring in a tractor and say that it's too noisy-but "too noisy" is subjective. Kubota doesn't pay for exploratory surgery unless there is a 100% chance that something is wrong or broken, but some folks can't realize that and then they get upset because teardown costs are the responsibility of the tractor's owner-UNTIL a problem is found. No problem found, owner is out a chunk of change to reassemble it and the same noise will still be there, and many times they'll say it's louder than it was because they're "hearing it more"; even though it's the exact same as it was before teardown/inspection.
Some older Kubota's used really big heavy flywheels to counter the vibration and noise, and it worked. The L3301 and 3901 do not use that big flywheel. It's plenty big (and heavy) but it's not 100lbs, I think it's only about 37 lbs if I remember correctly. I've got one of the big ones out in the shop under my bench grinder; and it works great for that.
4 cylinder tractors wouldn't do it nearly as bad because the frequency of cylinder firings is higher and there is less speed change between firings. A single, twin and 3 cylinder does, however. This is why the most popular automotive engines are V6's and V8's, the firing pulses are much smoother and therefore not felt (they call it NVH, noise/vibration/harshness). A 4 cylinder car, the vibration is always there and is part of why a 4 cylinder always has that sound and feel.