I've never been able to understand the whack the dowel through the board idea - perhaps its because the boards we use here in Australia are far too sturdy to whack anything through. We pre-drill everything when we are using central dowel system. Presentation board is normally covered MDF - under each cake we would have a STD board (which is the silver coated thick dense card - not the hollow flute type nor foam core) if we are using polystyrene dummy separators they would be drilled as well as the boards they sit on. The dowel is glued into the presentation board (another smaller board would be underneath to act as a cleat)
Once the cakes are ganached and covered they are lowered OVER the central dowel into position - sometimes it is easier to push a dowel through the top of your cake in the required position - it just leaves a neater hole that when the dowel is being forced UP through the cake.
Central dowel system used a lot here - I have delivered 5 tier cakes fully assembled on windy, bumpy roads with no issue. Yes it is a properly constructed cake which helps this but the central dowel makes it really easy to ensure that the cake is perfectly aligned - each and every tier.