I have two thoughts on this. First, I have to agree that it is strange when you finish a Kartos track, see you are at one end of the level, and then magically jump back to the start. But second, I don't know if I'd like it if I were suddenly in a totally different part of the level.
I think this could work if - after beating the track - Kartos simply offers to transport you to the other area. I think at the same time we would want that other area to have a sign or something that you could interact with, "call" Kartos to you, and navigate back to the original Kartos spot. Hmm, the more I think about this the better I feel towards it. It would just have to be handled right. I don't know if Playtonic is interested in making a change that big, unfortunately
We'll have to wait and see what this patch looks like. But the game did miss out on one of Tooie's most convenient features, the warp pads.