On the physics side of things, if you look at the Line II software* inputs you put in the semi-span dimension for calculating the line rake. Also the weight, expected flying speed, etc. So it does affect where the leadout goes. But since we invariably find the sweet spot by fine tuning (which is why you put in the adjustable guide in the first place) it's not like this effect would be noticeable.
On a deeply inset guide, I like to line the "tunnel" with 1/64" plywood. A wipe with thin CyA wouldn't hurt either.
Dave
*--Available on the NCLRA website