One of the problems I've had on long rides in the wet before is that my knees get irritated by the waterproof trousers rubbing over the top of the knee cap.
Shorts are not the same as trousers.
Trousers have a considerable length of material between ankle and knee to drag, especially when there's a bit of dampness to encourage it to stick. They also are frequently tight or fastened around the ankle to keep the end out of the chainset.
As a result, the material across the knee can be under a fair bit of tension when the knee is bent, which provides extra friction for skin irritation, and may also cause the kneecap to be dragged about in a manner that may cause eventual problems.
5 cm or so of loose material extending past the bent knee is under no tension, and is very unlikely to cause any problem.
On the other hand, as I said back in August, when the top of the knee is exposed at the top of the pedal stroke. it gets wet. At the bottom of the pedal stroke, the end of the shorts leg drops down over the wet knee, getting the inside of the shorts leg wet. It then drags up as the pedal rises, spreading the dampness up on to that part of the leg that is covered at the top of the pedal stroke, which in turn gets the inside of the shorts leg damp higher up.
Spend a long time pedaling in the rain, and the dampness spreads right up the leg.