It sounds like the GPIO is going to turn into a "big mess", because without a default connector, various people will put different connectors on top or bottom, thus all 3rd-party boards will need to be built for both situations.
Suppliers of add-on boards can deliver without pins or sockets soldered on so end users can solder in whatever they need to match what they have chosen for their R-Pi. It's only when end users and add-on suppliers each choose incompatible solutions there is a problem.
I'd suggest as a defacto standard of female sockets on top of the R-Pi, male pins under the add-on board or, better still, stacking header pins so the female socket on top is replicated on top of the add-on board - but you can't enforce that, only suggest people adopt it.
If there is a need for pre-soldered units which just plug together I expect enterprising third parties will buy-in R-Pi and resell with add-ons ready to use to fulfil that demand. There will likely be all sort of commercial ventures springing up to help the R-Pi community, from "send us your board and we'll solder headers on" to providing complete ready-to-use solutions. If there's enough demand the board manufacturers may even sell boards with or without header pins or sockets.