Permanent magnets need to be raised/lowered away from the un-coupling position so they act like electro-magnets . In the past I have used 1/4"/6mm ones sliding up/down in K&S tube, and worked by servos, an idea gleaned from Stuart Bailey. I think if I remember correctly that Ian Morgan uses a similar arrangement with the magnets on hinged flaps.
Here are acouple of shots of my arrangement. Lowered and raised. The magnets sit just under the sleepers with a thin layer of paper between- to hide them and allow for ballasting. All very crude as usual for me, but it works, which is all that is needed.
This particular one is for two magnets on adjacent tracks. I have arranged up to four across a baseboard - saves on servos.
hope it might give you some ideas
Here is my arrangement under Freshwater. This one covers 3 parallel tracks. I drilled very small holes between the tracks so I could see where the magnets needed to go. The baseboard is something like 3mm MDF.
The servo arm rotates so it changes the axis of the magnets rather than just lowering them. The magnets need to move quite a long way away to ensure they do not cause unwanted uncoupling. In fact, I have since modified them so they rotate to nearly 90 degrees now. I have also replaced the Merg Servo4 modules with Merg CBus and CANSERVO8 modules, but that is another story.
I am sure these magnets would work through much thicker baseboards.
Thanks for the suggestions guys - definitely food for thought.