In general, I do not like stacked pins either. When I'm probing pins on the actual PCB, I also want to be able to find them in the schematic, and thus my opinion does not coincide with the recommendation in the KLC. Pin stacking does make more sense for bigger BGA's. First, then can have 100+ power pins, and those are not even visible on the PCB for probing.
And then, there are also SMT mosfet's which have several paralleled pins, and showing 8 pins on a schematic for a 3-pin device is also a bit bonkers to me. For such MOSfets, I tend to modify the footprint so it uses only 3 pad numbers. In KiCad, when different pads have the same pad number, you have to connect all of them on the PCB for DRC to be happy. And for such FET's it's usually easy to see on the PCB that pins are paralleled. Pad numbers are also not only numbers, but 4 character alphanumeric strings. This is needed for BGA's and such with "chessboard coordinates" For a MOSfet in an 8-pad footprint you could name the pins "G", "S", and "D".
I guess the best approach is to do it neatly, but accept that perfectionism is not attainable, and attempting to achieve it is a huge time sink for little additonal benefit, so don't overdo it.