Media Center should be pulling down both the "Aired Order" and the "Absolute Order" to separate fields, with absolute order taking priority for sorting.
We could probably pull that info in somewhere, but it doesn't seem to be filled reliably everwhere, especially when it comes to in-season full episodic specials (like Doctor Who Christmas Specials)
What your views sort by is your own choice though, really.
The question also is when those fields are filled and/or changed. When a show originally airs in one order, and is then released in another order on DVD/BD, the Absolute Order may only then be changed to match the DVD order, and you wouldn't be any wiser, since you don't go around updating your shows all the time.
If we had such a field, we could also try to make it lookup over that if Season/Episode is not filled, which would probably work assuming that Absolute Order and Season/Episode never desync - but given the example above, I think it could possibly desync at some point, which would leave the question - what do I prefer for lookup, absolute or S/E? Probably S/E, since thats what we've used for ever, and its not going to change for existing episodes, while the example suggests Absolute might.
At least you could fill Absolute using the "Fill from Filename" tool and then lookup over that, making the whole process a bit easier.
Additionally: what are we supposed to do about specials?
I recently added a show which had some "special episodes" and I couldn't figure out a way for MC to download the information for them.
TheTVDB sorts specials into Season 0, so find out the Ep number to go with that, and it can pull info for that.
With specials not filling Absolute Order either, that unfortunately cannot really be automated any.