The licenses you bought on the Mac App Store are non-transferable, as you already found out. The license for the preinstalled copy CAN be transfered, but only as part of a transfer with the original hardware it was installed on.

Therefor the only thing you can do when selling your old computer is delivering it with the original software it came with. Anything else would be a violation of the license agreement, and can be considered as software piracy.

update

It's was just a glitch in the App store, the applications had been installed, it seems one hand doesn't know what the other is doing.