I think you are misunderstanding the home concept with the breakout board/linuxcnc.
-linux cnc starts a home command move (from the main linuxcnc screen) -moves one of the axis and waits until the home switch on that axis closes(which is connected to pin 11 in your case) and then knows it is homed.
setting the X home position to 100 means after the home move, linuxcnc will identify the current X position as 100 after homing
I set my 0 X limit as my home and after i home the x then the x displays 0.00. and the table has moved to its right direction limit(it helps that i used the switch on the lefthand side of the table!!)