Logically, they should award in favour of the driver who qualified lower in a tie-break, but not because they qualified lower - it just turns out to be more logical!
If you're sending drivers down the order, you don't do it in a vacuum - it has the consequence of moving other people up. If someone qualifies 5th and loses 10 places, you don't declare that there must be a tie-break between them and whoever actually qualified 15th. You just physically move them down down places and whoever qualified 15th will end up 14th. Note here that if you do view it in terms of a tie-break it's the driver who initially qualified lower who takes precedence, so that should give you a clue for other cases.
To look at a simple case, pole guy gets a 2-place penalty and 2nd gets a 1-place penalty. Using the FIA method of adding numbers up in a vacuum, they both get given position 3 but then the original pole guy wins the tie-break and ends up 2nd, so escapes half his penalty. The guy who initially qualified second would have started first without his penalty, so he's effectively been given a two-place penalty.
Using the logical system, you physically move them both one place back to start with (use toy cars if you want) and they end up 2nd and 3rd with the original 3rd guy now 1st. The original pole guy still has to go back one further place, so he swaps back down to third with original 2nd guy now second. This is logical, because you view their penalty in terms of where they would have started had they not got a penalty. Both drivers have been given the appropriate penalty.
This is not what the FIA do of course, because they've tied themselves up in knots with it and have no idea how to extract themselves.
That's the way.
