To answer the question, "What is exactly N% of top hands?", there really is no correct answer as it depends on the stage of play (i.e. Preflop, Postflop) that's currently occuring. Specifically, it isn't VPIP/PFR.
Making use of these programs and hand-rankings is a matter of hand reading skill. The hand-rankings are a generalization of how a player should enumerate the plausible combinations in their opponents range according to the situation at hand.
Just as the Pokerstove FAQ mentions, hand-ranking systems are arbitrary because the nature of the game will rarely, if ever, present players with situations that conform to linear orderings of hand equity match-ups. To put it another way that's well known, "it depends"!
Looking a little deeper, there have been a number of methods used to rank hand match-ups according to differing scenarios, preflop and postflop.
Pokerstove uses, as they mention, an arbitrary measure of All-In equity vs. Three random hands. What is commonly called hot-and-cold equity, as it relates to showdown equities without any extra raises or folds involved, from any street onward. The full equity breakdown is found in a zip file through this page here: Holdem Preflop Match-Ups.
Other hand-ranking systems such as Sklansky-Karlson (aka. Sklansky-Chubukov), the inception of which is here: The Sklansky-Karlson All In No Limit Holdem Rankings I believe relate to a limited game of SB vs. BB dynamics and specifically push-fold ranges, more suited to tournament scenarios.
PokerProTools uses an "evolutionary computer simulation, whereby the set of "good hands" is gradually refined, and hands are ranked against other "good hands"". It's based on a scientific papers findings (The Challenge of Poker, Billings et al.). I've skimmed, and read over this paper a few times and, as you'd expect, it's a dense scientific piece of writing but still carries lots of insight in plain English about determining relative hand strength. This is where I found it some time ago: Towards a Meaningful Ordering of Hands
I'm sure there are more rankings systems than these, as I can recall a few being mentioned on Poker.SE already, but these are probably the most referenced versions.
I came to realise that good observation of your opponents tendencies should cause you to create detailed individualised hand-rankings based on your opponents play, and that these systems are good as starting points, but won't ever be definitive examinations of what your opponents are doing in real time.
