The definition of a Stack on page 9 of the manual states:
“if a Robot is touching a Cone on a Mobile Goal, that Cone and any above it will not count as being Stacked.”
Does “any cone above it” mean cones nested on that cone or does it mean cones physically farther from the ground on that stack?
In other words, how does this rule apply to tipped stacks or even upside down stacks?
These are some very good questions, Captain Picard 
It refers to Cones nested aboved the Cone being touched.
The intent is for Stacked Cones to only count on upright Mobile Goals. Thus Cones nested on tipped Mobile Goals or even upside down Mobile Goals would not count. Please note, Stacks on tilted Mobile Goals (e.g. if a Mobile Goal is resting partially on top of a Zone pipe) would still count.
We will be addressing this in the June 15th update with precise wording to make this clear.