Am I just paying more attention to these details than most people do?
Probably, but when you've played lots and lots of games, things like these are more likely to bother you; details bother me too at times, but very rarely on my first playthrough.
Making physically realistic levels is generally hard because there usually isn't a practical way way to 'test' their realism: you could use some physics simulator, but the higher degree of accuracy required, the longer the test would take because of all the calculations needed. Add to that the fact that the majority of players doesn't care enough about that to quit playing, and you'll see that it's not worth the effort.
Of course the degree of realism expected of levels largely depends on the type of game. If you're making a KS Environmental level that has recognizably realistic elements, you'll want to pay attention to details, because that's one of the main reasons players chose to play the level in the first place.
All in all, games are just a set of rules and a goal to accomplish. Modern videogames have lots of rules, and illustrate most of them as the player goes through the game, a lot of them implicitly (can't have Juni go through walls, enemies kill by mere contact, etc.); if the level builds up some kind of expectations in players, the level author has to make sure they're met throughout the whole level (with some exceptions, I guess). So if you make a level that encourages players to pay attention to realism in setting, graphics, events, or other elements, you have to try not to break their expectation further into their playthrough.
Going for realism has its perks because it's something most people recognize, so it makes the level more easily accessible, but on the other hand it's harder to make, as it imposes limitations that often go against the limitations of the game engine you're using, and may restrict the rules you want your level to have.
Is it necessary to have things that don't make sense to make a good level?
Probably not, but it's definitely much harder because of the additional constraints you have to work with. A quick example: instant teleportation or fast travel. It's nice to have in exploration games so you don't have to worry too much about the player getting bored by having to backtrack a lot, but you can design your level so that's never needed. Alternatively, you can employ a method of fast travel that's believable, that players can find to be realistic in the setting chosen for the level.