The proposed docking mechanism matches the one I'm already using almost perfectly, but we're going to need more coordination when the magnetic-only docking comes along.
Right now I'm just assuming that a hermaphroditic docking port is going to have to extend out from the hull and have a little space between the collar and airlock, and it's going to need the most specific planning.
A female docking collar would likewise need to extend out from the hull. It can be set on a rail that extends/retracts the docking collar on demand. The reason it's female is that it needs to possess the rail basic blocks to dock to in order to accept other craft, so you're docking a big craft to a little craft on a rail to another ship, which might pose problems when docking extenders come into play again, which I assume will be used to allow a craft to accept something with a lower than 1:1 mass of parent:child docking situations.
A male port needs a rail docker block, and can be flush with the hull or extended by solid hull; the game won't let us chain dock with two parents, though, so we can't have a male port that extends outwards to dock to a port on the other craft. That would require it to be docked to two entities simultaneously, or you'd be using a female port and the other craft would inevitably have to dock to you.
With the female port you can put a rail on each of the compass directions, such that you can choose which direction is the most ideal orientation by moving the child ship around.