Not sure I understand what you are asking.....
The MDF is the presentation board and I would normally cover that with food grade vinyl (normally novelty or something that perhaps required a black base) Wedding cakes always have fondant covered boards. Each cake sits on its own separate STD silver board, even the base one (so at no time would the cake come into contact with the MDF - the dowel I use is brush box which is used to make chopping boards so it is food safe - but even then it would barely touch the cake as the predrilled boards and the coring means that there is a mm or two clearance
I still have skewers under each tier
I can't say that I have ever tried the hammer it trough the top technique but for me I think there are too many areas where it could go wrong - ie hard to work out the centre, worried about card fragments in the cake where it has had to pierce through, not being at a true 90degree to your board and not having your central dowel secured to your base board
I think it is just one of those areas where I say... if its working for you and you are happy with it - continue doing what you are doing. Same goes for me