You surely can design an expansion board that goes on top of Bela, in fact we do it ourselves for our capelets.
Some care will have to be taken about hardware mount for board-mount pots and foot switches: you probably do not want the whole three-board stack to be suspended by the mounting hardware for the footswitch and pots.
I would discourage board-mount footswitches, as I see how the durability of the board could be seriously compromised by it.
If i was to do this, I would probably opt for panel-mount footswitch, switches and pots, especially considering the only external component you need is going to be a resistor for the switches.
Also, make sure you look around the market to see if a stompbox case of the appropriate size is available around.