Awesome game so far, I am enjoying the hell out of it. Though there have been a few issues here and there and maybe a few solutions which seemed a little wonky enough to question if they were intended or I missed something - but that's another matter.

So I just finished the last De Gerlache area to hit the switch. Question is mainly regarding something in the very last level section with the two tall towers where you start with Phi and Omega that you eventually turn into Sigma and Lambda.

Now, not sure if this was a developer oversight, or if I'm misunderstanding something that will be explained later, but here's the impression I'm under so far:

-It would seem that you can't have more than one box of the same Greek letter within a level zone, and if you attempt to "make" another by, say, putting a blank box in an Omega holder when there's an Omega box somewhere in the level it simply doesn't let you (you can put it there but nothing happens, and you can usually tell whether there's one somewhere or whether you need to make one depending on whether you see "Teleport" or "Insert Box").

-Probably because if it did, there would be more than one option of a box to summon with "Teleport" and no way to determine.

-By "level zone" this seems to be any area starting with a blue gate that turns red behind you, and ending with an exit to the following blue gate. Sure, some of these areas have multiple sections, but a zone where a Greek letter box must be unique to, is defined by that, and I believe also "restart" would take you all the way back to when you entered the blue/red gate and those are the only checkpoints.

All correct so far? Now, here's where I'm confused.

So as I said the first part of the level involves solving puzzles to eventually turn Phi and Omega boxes into Sigma and Lambda respectively, and then access the towers, which are supposedly still the same level - after all there hasn't been a blue gate, and we've been ferrying over the Lambda box which we can still summon.

However, the confusion is that there appears to be an Omega box at the top of the tower - which was apparently there the whole time.

Since the towers are part of the same level-zone from the first area where I started, if I understand correctly... with the Omega box available in the beginning, there were apparently TWO Omega boxes in the level at the same time the whole time, before I changed the first one - how is this possible, and what prevented it from summoning the one from the top of the tower?
Sure it's far far out of the way for the player to know it exists while we have the other Omega box, but... as far as I know, it still exists, which creates an inconsistency,

Is there a mechanic I'm unaware of or misunderstanding (or, long shot, have yet to learn) that makes this possible, or was this an oversight?
If there was a blank box there next to an Omega portal that we had to make, THEN it would maintain consistency - but there wasn't, it was already there.

Any explanation for this? Sorry if it was confusing. No spoilers please.