Mt pilatus

That doesn't seem like adequate time to me. If I'm reading your post correctly, you're allowing about five hours for the whole trip, which seems a bit rushed. I'd suggest spending a bit more time exploring at the top. Rather than have a packed lunch, you could buy a fine lunch in one of the restaurants at the top and spend some time enjoying the views.

I made the trip in the reverse direction, taking the boat to Alpnachstad, the Pilatusbahn cogwheel, and then the cable cars down to Kriens. I don't recall having to get reservations for the cogwheel, but of course that may have changed since my visit.

Suggesting that people make reservations is becoming more common as the crowds continue to grow. This year there are quite a few mountains that have added that feature.

I agree with your own thoughts, it sure is hard to guess when you might want to move on. All I can suggest is to give yourself more time than expected. If you are done early you can see if there is room on the train for you, if not at least you have your reserved spot. I think that the main idea is to reduce waiting times, pretty sure that people do not get stuck at the top unable to ever come back down :-)

I almost always bring a picnic lunch when I go up mountains for hiking or just to enjoy the view. You can always get something to drink or a snack from the restaurant as well if you want to (the fries are usually delicious!). Just be sure to look for a place to sit that is not part of any restaurant’s outdoor seating area when you eat your picnic and you will be fine.