There's a significant chunk of wisdom in not over-specifying. Is there a significant need to plot out the *exact* route the bad guy was taking beforehand? If not, then don't do it. This leaves you room to flex when the players come up with reasonable suggestions.
I think it would be improbable or impossible for a GM to fully detail any area, let alone a large area to the finest level of detail for him to KNOW the actual answer if something exists or not at a given point. In short, he has to make stuff up when the players ask.
This in turn ties to the keyword Story that the OP used in the OT. I'm glad it didn't get dragged out, as it's not a Story issue. It's an information issue, which is the same problem for a sandbox GM who eschews story. In fact, one could argue, that the more detail the GM plans out, the greater risk of RailRoad behavior could kick in (RRing being a trait of planning to much on how things HAVE to be).
Narrative Control to me is in effect dictating what happens next or what actually exists. Forex, the player saying "I race out into the street after the BBEG. Seeing he's getting away on a horse, I pick up a loose cobblestone and throw it at him. It hits the flank of his horse, and it rears up, throwing him to the ground. I use that to catch up to him and cuff him."
The player invented content (the rock, the horse), dictated what he saw when first leaving the building (BBEG on horse), and dictated the outcome of his rock throwing attempt.
I suppose there's some kind of game where that's OK, but in most flavors of D&D:
the GM decides what the players see when they get to the street (BBEG on horse)
the player asks if there's a rock he can throw (GM decides if there's a loose cobblestone)
the player tries to hit the BBEG (attack roll with rock and hits)
the BBEG must make a Ride check (he fails)
players do not have perfect information. Nor are they in control of outcomes. Therefore, everything they say is really a question.
When they ask for a rock or a shortcut, the player is seeking the same information the PC has. Does it exist? They are not creating matter from nothing. They are seeking information.
The GM, lacking details on whether there's a rock in the PC's current square or not, has to determine that. He is always the one creating objects in the game space, not the player. But in his case, he simply does not waste time creating objects he doesn't know he needs (he may very well have never thought the PCs would be chasing the BBEG in the street, let alone needing to throw a rock because he left his crossbow at the hotel).
If the player asks "Can I throw a rock at him", he's actually seeking a number of details. Is there a viable rock around (and not a useless pebble)? Is the BBEG close enough to hit, or is it pretty obvious he's out of range? A good listener realizes there's more to the question or proposal, and tries to account for it.
In the case of the shortcut, if your map is like mine, as a GM, you might not actually KNOW the answer. So you really do have a choice to decide if it exists or not. If you decide it exists, you might then make the PC do a skill check to see if he knows it.
You could interpret that to mean that it does not exist if the PC does not succeed at that the PC created it. But that's BS. The GM determined the conditions for the PC to know of the shortcut and thus the GM still determined if the short cut exists by way of allowing the check in the first place.
As for documenting and rembering this shortcut? How big a deal is it? The PCs are running from point A to point B. Odds are good, they will never need to run from point A to point B again. Instead, needing to run from B to C or A to D or C to D. This need not be a big deal.