Not quite sure what you mean not being able to place in some locations/rotations you want. You can only place in three main directions
⬜️🅱️
⬜️🅱️
🅰️🅰️<-🅱️🅱️
⬜️🅱️
⬜️🅱️
But they can also connect sideways if there is an allowed "root" bone to connect to. Ie. you could place B here attaching to green and it would allow to make a loop to A.
⬜️🅱️🅱️->❇️❇️
🅰️🅰️
And obviously the other side also needs to be the correct value to allow for a connection.
But yeah, there is a bug with the rotations working kinda wrong when quickly changed ending up with rotations that are a bit off (didn't happen inside unity editor so I didn't catch it) which can result in some weirdness. I've fixed it already but can't push an update before the voting period is over.

All right! Replaying the game not as tired like yesterday was much better :) So yes i got the point of getting more and more limitation with the skulls and makes sense so it limits the user choices which might be too big after some time. I have found another kind of placement thought which i was not sure why i cannot have (see above). Why i cannot place the 4-1 between the two 4s? (not intentional but you see the bug is hiding some important detail :) under the bug we have 4 too). Maybe limiting instead of skulls it can be a map or a dungeon kind of thing where you can continue to expore and maybe bigger / smaller rooms are available that would be maybe more interesting and get the same effect as skulls? Anyway really cool game.