Interesting stuff thanks.
Generally speaking, when I'm planning daily itineraries on Europe trips I try to work out travel that takes half a day. It's off in the case that we are arriving at new destinations an hour or two before hotel check-in times. Of course 90% of the time your rooms are ready, but anyway they can take the bags and hold them for you if need be.
Sometimes we end up with longer travel days, particularly if we are making a transition from one country to another to start a different part of the trip. Or if there's a place we really want to go and see, and the only way is to burn basically a whole day transitioning and traveling.
But generally I plan so that we arrive in a place for lunch or in the early afternoon. Since we've been sitting and relaxing on the train trip (hopefully! - there's a spectrum of experience to be had on the train), we feel energized to go do a couple things that we would like to do in the given location.
The tension for me and my planning is usually how early do we want to get up, and how quickly do we want to get out the door. I always involve my family in these decisions so they have some buy-in if they choose to get up early. Usually it's not at all bad getting out of bed to make, say, and 8:00 a.m. train. If one does one's self the favor of seeing planning as an holistic future reality, not just cells on an Excel spreadsheet, then one ends up selecting accommodations that make earlier trains easier, planning the previous night and day to feel satisfied with a bit of an earlier turn in, etc.
I think the greater point of the op is well taken. Travel is not just travel, it is also transitionary time. So a 4-Hour train journey can effectively take nearly the whole day. As such give yourself a bit more time at destinations that might be impacted by travel days.