It'd be more balanced cool if the teleporting rails cost an ender pearl each time they teleport a Minecart entity. Fuel could be input in the same GUI as the colour identifier selection, and also hoppered in using a Minecart hopper or regular hopper. Minecart hopper could be allowed to stay and function as an input to the fuel slot when the rail is powered, or maybe vice versa - requiring redstone to teleport.

Having a cost for teleportation sounds good, however, I think the thing with the hopper carts staying is complicating things a bit too much.

I'm adding a block to ShadowMC that functions as a capability proxy. It could be placed directly under the rail allowing hoppers and other automation to input pearls into the rail via the proxy block.