Yeah, it was a bit disconcerting in my first playthrough and it's even stranger now. Palaces 1-3 have the most shortcuts and stuff. There is more verticality present in them which allows for stuff like elevators to be used.
The 4th and 6th ones are a bit special in a sense since they have a "hub" of sorts where the player goes back every time the finish a piece of the dungeon. The 7th one doesn't really need them due to the structure.
And the 5th one isn't designed with those in minds.
I don't think this would be part of a troubled development. I was thinking about people being scared, or bad at stealth, and getting kicked out of the game on Calling Card day because they hit 100% Security Level and they didn't thought about using a smoke bomb to reduce security level. I have to say sometimes I've had to go through the dungeon to open some locked chests and it wasn't that bad.
The game is pretty forgiving when it comes to stealth (I mean, enemies don't notice you if you move between cover spots). And, if that isn't enough, there is a Confidant that nerfs that mechanic as you level her up.
I was thinking of this change more as a focus test thing TBH.
Maybe I'll try to do the Calling Card parts that way when possible