The design of electromagnetic track brakes has alternating polarities in order to increase the effectiveness of the braking force. What is the fundamental reasoning behind this increased effectiveness of braking force based on alternating polarities?
Each pair will act like a horseshoe magnet with the rail acting as a "keeper" which closes the magnetic circuit and will result in maximum friction.
The alternative is to place all the same poles touching the rail with the result that the flux path to the other pole must travel through the air. The permeability of air is about 0.001 times that of iron so the force of attraction is greatly reduced.
The brake works by converting motion to current, and current to heat. The current in this case will be vertical, as it is perpendicular to both the motion (forward) and the magnetic field (horizontal).
If the magnets are all facing the same way, they will maintain a DC voltage from the top to the bottom of the rail. This is interesting, but doesn't dissipate much energy. The first couple of magnets will drive most of the current, and the remainder simply reinforce the E-field.
Alternate them, and you get an AC current in the rail. Each magnet can induce a fresh current in the opposite direction, forcing the electrons to the opposite side. This way, each magnet contributes to the overall braking.