In the same way burning straight off Pentonville allows the middle system skip is it possible there are other similar skips? Does the game always orientate the ship "north" with respect to the nav map when undocking from a station or jumping or is that a coincidence limited to Pentonville?

I've tested this by launching from various places in the savefiles I have lying around, and we always do get placed "north" of the dock when we launch. Even when that position is a little bit silly (e.g. Helen in Troy)

Aferburning out about 25000m from Pentonville just to skip the middle navpoint wouldn't normally be worth the bother - it's just that we have to get clear of the asteroid field anyway. What makes this skip worth doing is the combination of a middle navpoint, the asteroid field, and "north" being approximately perpendicular to the direction we want to go in, and I can't think of anywhere else that has all that.

Skipping the middle makes a lot more sense if the middle position is hard to deal with. Which is to say, asteroids. There may be some room for improvement here...

Xytani: Instead of going from one jump point to the other, go to the other nav point first, turn 180 and burn until clear of the asteroids, then autopilot to where you want to go. We'll have to deal with whatever spawns in the spare navpoint, but we'd have had to deal with whatever spawned in the middle asteroid field anyway if we did this normally. This seems promising, since we no longer have to burn all the way through the asteroid field. The possibility of getting the Steltek drone makes this a gamble, and probably a bad one, when returning from Rygannon. It should be fine when going to Rygannon, though.

Pender's star: On arrival, point yourself 90 degrees away from where you want to go, burn until 17000m from the jump point you arrived at, then autopilot to where you want to go. This replaces a burn through an asteroid field with a similar-distance burn through open space, and also skips one autopilot cutscene. I'll have to time this to see if it helps, but I'm only expecting to gain a few seconds here.

Gamma: we could skip the kilrathi encounter between navs 1 and 5 by going via nav 3 or 4. Not sure if this is faster than talking them down.

I do do a similar skip when I leave Siva - in this case, using an invisible navpoint to skip another invisible navpoint that contains asteroids.