It makes sense because it follows the rules laid out before you. I get that you're annoyed because you somehow misunderstood those rules, but it's pretty clear both where you're going and why at that point.You also were did NOT stand on it when the two planets had aligned, as you can only do that when you're in the eye of the sand tornado, which is pretty clear. All of the towers are pretty clear about where they're going once you understand the system of them, and there is text all over that explains the ash twin project and that you need to use those towers to get to it, and that it's inside the ash twin. I guess what I'm saying is, if you didn't get the solution it's not because it's poorly presented, but because you simply weren't putting 2 and 2 together with all the hints out there, same as if you hadn't figured out like, how the gravity crystals work for example - the information exists and you should've seen it by then, but somehow you didn't.
I get that there are hints and it seems clear that the other tower should be used for something, but I disagree that it follows the rules... The way it works in other cases is you're warped when the black hole pad is aligned with the white one, and you're always sent up from the warp pad. In this case though, I guess the black and white pads are always aligned, since they're on the same planet. It just works when the pad is aligned with the Ember Twin, for some reason, and you're sent down instead of up.