Welcome to Tree World Durandal.
It is hard to say what EXACTLY caused the dwarfism in your maples, but I can make an educated guess based on the info you gave us.
In simple terms, it sounds like the plants in the plastic lined baskets were kept under constant stress by being water logged. Roots need oxygen. Water displaces oxygen in the soil. Not enough oxygen to the roots and the plants may not develop properly. Conditions were probably just shy of being enough to kill the plant.
In my world, in the landscape, people will do this on purpose. When planting a tree a nice big hole is dug, and the tree is planted with the top of the root ball well below the surrounding grade, like in a bowl, so the tree can get "plenty of water". Has the same general effect as your plastic lined baskets. I will spare you what I call this.
I would encourage you to experiment all you want. It is fascinating how plants adapt and react to different environments, and there is nothing like seeing it for yourself. Maybe do some research on bonsai. Maples are a good plant for this technique.