You're counting empty net points against him? He's on the ice at the end of the game with a one goal lead, shorthanded (empty net) to preserve the lead and get a win. Where is Matthews at the end of the game with a 1 goal lead while the opposition has an extra skater on? ... And if Marner gets Matthews money, YES, yes, they will both be overpaid.
Matthews is the bigger name right now. Had your glorious GM signed him for 10.1 (the 4 1st limit last year) he would have laid the groundwork for similar with Marner. Now? Who knows but I have to think 10.5 (projected 4 1st limit this year) until he is UFA is the starting point now. With somewhere between 200k and 500k per year for each UFA year you eat. Which (happy for you) is less than Matthews.