Lots of different info here, hopefully this will clear things up a bit:
Both Shimano road and MTB 10-speed chains use the same 10-speed pins to join.
The main difference between Shimano road and MTB chains are the position and shapes of the plates due to the difference in chainring and cassette sizes when comparing road to MTB. The inner links on MTB chains are also solid for increased strength.
If a Shimano chain has a short pin in it, this is an OEM pin which is usually fitted in the factory using an air gun. I would recommend removing this pin and fitting a snap off pin as it is very difficult to get the short pin in the correct position using a regular chain tool.
Hope this helps.