Answered: Clarification of Stacked

Under the definition Stacked Note 1:
Cones still count as being Stacked even if the Mobile Goal that they are Stacked on is not Scored.

A robot carrying a Mobile Goal with cones stacked on it, will the Cones Stacked on the robot count at the end of a period?

Assuming you are referring to Cones that are stacked on the Mobile Goal being held in the Robot, and the Robot is not contacting the Cones at the end of the match, then yes, those would count for (2) points apiece.