I can't see any good reason why cup pushrods would be measured any way other than overall length. The ball end measurement isn't subtracted so why subtract the socket depth? I'm sure there's a good reason.
Cup depth from the lip to the bottom may vary and the "effective" length is the actual, physical, mechanical pushrod length, like the overall length of a ball/ball pushrod. The cup does nothing more than locate/capture the adjuster. Stamped rockers have the cup built into them.
