I don't think using wickets lost is a great tie breaking method to be honest.
Teams have 10 wickets and 11 batsmen for a reason, they are there to be completely utilized if required.
You look at the last two balls of England's innings. We managed run outs on both. They could afford these run outs because they had wickets in hand, and resources that could still be used.
Any metric used to determine a winner in the event of a tie is going to have its flaws, and be somewhat arbitrary. Unfortunately we ended up on the wrong side of it today.
Completely agree with you on the calls to do it on wickets in hand - it is just as arbitrary as boundaries, for the exact reasons you mentioned. England 'earnt' the right to concede those runouts from how they had performed during the rest of the innings.