That is true, you need a way to deal with skills over a hundred when using high roll wins.
Simply halve both skills until they are both under 100...
(NOT!)
The way MRQ deals with it (after two updates) is to add your skill over 100 to your roll to determine the winner of tied success levels. So if my skill is 140 and your skill is 120, and I roll a 72 and you roll an 85, my roll become 112 and your roll becomes 105 for purposes of deciding a winner.
At that point the "makes roll by most" method is almost as simple, though most people find addition easier than subtraction.
I used the makes roll by most method for a while as I am not afraid of simple subtraction (also known as "complex math" on various boards) - but must admit in the end I switched to just using highest roll wins as it seems simpler in practice at the table. It becomes second nature in short order.