My suggestion is to start measuring from the top of the base, which is part of the connector. The outer part of the connector is shielding the actual antenna element in that section, so it should not count in the antenna length...unless the manufacturers instructions dictate otherwise. I'm not sure of the internal construction of the antenna.
As for collapsing from the top or bottom, I would start collapsing from the top. This will keep the antenna's taper as smooth as possible, which is better for both reception and overall strength.
These things being said, in the end you probably won't notice much of a difference in reception no matter where you start measuring or collapsing from.
-All the Best