A 6 cylinder is not perfectly balanced. It is in the first order but that's it. There is a whole engineering subject on that topic which I won't get into.
A 3 cyl is MUCH cheaper to manufacture, and it runs fine for their intended purpose. Intended purpose is small equipment that employs some compromises for the end result of lower cost, shorter hood line, MUCH better visibility, quiet operation, and acceptable power output to name a few.
I used to have a hobby 4440 JD, 6 cyl, you couldn't see anything that was closer than 20' in front of the hood. No loader, just tractor. A lot of the old Deere's were 6 cylinder. Yeah they were smooth running but you gave up a lot. That's one reason Kubota's M7's were just 4 cylinder engines. The M8 is a 6 and obviously quite a bit larger physically.