Counterstrike doesn’t get the Ob penalty because it’s about using the opportunity created by predicting your opponents action and capitalizing on that opportunity. Fighters aren’t stationary at their weapon ranges, they’re always circling, probing forward, and dropping back. Counterstrike is about using defensive footwork and weapon-work to exploit your opponent’s aggression.
From a design angle, applying those penalties to the strike portion makes Counterstrike pretty untennable. While Counterstriking cleanly is a difficult move, best reserved for use against less skilled opponent’s, that difficulty is already represented in the need to split your dice pool; of you split fifty-fifty, you need to be twice as good as your opponent to reliably make their attack a wash. If you then needed to overcome the Ob penalty to strike, you’d have to be a super-martial-artist to make the attempt worth it in any cases where you didn’t have the advantage. In cases where you do have the advantage, your opponent is more likely to script defensive actions, so you’re less likely to get Counterstrike to go off in the first place.
Similar to what I was saying above, it’s more ludo-narratively cohesive to not apply the Ob penalties, because you don’t need to be a super-badass to have a shot with Counterstrike. In fact, the maneuvers that Counterstrike represents are the ones you’d want to use in a situation where you’re at disadvantage.
Lastly, strategically, Counterstrike gives release valve for the advantage system, and helps keep tension when advantage Obs are high. Because you might get Counterstruck pretty hard (difficult though Counterstrike already is) you might think twice before scripting as many Strikes as your WS allows. Maybe you’ll throw a Feint or two in there instead.
I hope that answers the question. Feel free to dig deep into anything I’ve said here.
As for engagement, positioning Obs don’t apply to defensive actions. The Obs hold until advantage is changes for some reason; this can be from Vying for Position, the Beat action, one of the actions that require use at Hands distance – Lock or Charge, for instance – someone futzing with their weapon(s), slamming a door in your opponent’s face, possibly some others.
You can think of Engagement as the first Vying for Positioning test, and of advantage as something that can be passed back and forth – it’s dynamic.