Nifflas said on Twitter that the master key exists for speedrunning purposes. It was also absolutely necessary for the recently held The Village is Lava competition, which required getting both endings without entering the village or unlocking more than two of the ZUG doors.
As for secrets not mentioned here yet...
Holding enter for a few seconds in the save room will cause one of several possible items to appear. You can get some pretty rare stuff this way.
If you activate developer mode by pressing F12 in the menu, you can go to any place you wish, including a few screens not normally accessible.
Two of them only serve to quickly trigger the ending cutscenes for testing purposes, but there's also a whole chain of puzzles that appears to have been made to test some of the gameplay mechanics. They are actually legitimately challenging and use some tricks that aren't really utilized much in the main game.
I get the impression the whole save room system worked differently in early builds of the game though. These screen all have teleporters that don't work correctly. Anything you put in them can't be accessed later on.
While developer mode is active, various additional objects will appear in the game. Their purpose appears to be to allow level designers to test their creations more efficiently by allowing them to cheat.
You can freeze the countdown of active time bombs by putting them in your inventory. Could be useful on some occasions, such as if you accidentally teleported active bombs.
If you press the key for a free inventory slot while standing on an object, it will be transferred there instantly without having to pick it up first.
You can put coins into your inventory by using the aforementioned trick. However, you will still collect them when taking them out of it. This could still have some uses though, seeing how inventory items aren't lost upon death.
You can actually carry coins if you pick them up while having 99 coins, seeing how this renders you unable to use coin-granting items. Don't see much of a use for it in the main game, but you could design custom levels with this in mind.
The violet gun is so powerful it can even destroy skull blocks, therefore removing the need to sacrifice animals. Probably not too useful outside of the prototype area though (which actually requires doing this) unless you're trying to minimize kills. Actually, that would make for an interesting challenge run, wouldn't it?
There is a detector detector [sic] hidden on a floating platform in the village. Doesn't really serve much of a purpose though unless you find it before you know the locations of the other detectors.
Teleport lasers are inactive as long as you have 9 items in temporary storage. Disabling a teleport laser this way is a perfectly viable solution for one of the puzzles that give you a red bird.