It turns out that I may have misunderstood - the same thing happens for me when telling MATE Tweak that I want to use Compiz rather than Marco as my window manager.
The switch to Compiz certainly happens (I am reminded of why I stopped using it..) and it is sticky between reboots.
So either it's not just a Marco thing or some part of Marco is retained when using Compiz.
It turns out that I may have misunderstood - the same thing happens for me when telling MATE Tweak that I want to use Compiz rather than Marco as my window manager.
The switch to Compiz certainly happens (I am reminded of why I stopped using it..) and it is sticky between reboots.
So either it's not just a Marco thing or some part of Marco is retained when using Compiz.