I'm not sure why this situation is confounding you.
There are certainly reasons why he might elect to stay in Toronto next year even if he was looking to go elsewhere as a free agent.
First and foremost, this is home and by his own admission he really likes it here. That , more than anything else, should "make sense" to you.
Secondly, as a pending UFA who wants to maximize his value, staying in a situation where you're playing with high end offensive players certainly makes a ton of sense for someone who wants to post the best possible numbers that they can in order to maximize their next contract.
Third, he simply may not have any interest in moving right now if he's going to end up moving again as a free agent in 12 months. It's in his best interest, if he's leaving Toronto (and I'm not at all convinced that he is) to wait until the summer, assess the situations of all the teams and then decide where he's heading. Why decide now, a year in advance, only to facilitate a trade for Toronto, which would in turn weaken the team he is heading to? It makes a lot of sense for the Leafs, of course, but I don't see what Marner gets out of it. He weakens the team he is joining and then he forgoes the chance to go to market and maximize his dollar value by signing an extension with the team that acquired him?
Why?