I just recently had this conversation with another a$$hat... What you obviously sacrifice when you violate geographic sanctity is the ability to operate exactly like the prototype (i.e., using actual timetables and train movements). That said, it doesn't make ops impossible...just means you have to make a few modifications.
OTOH, for a guy like me that is an unabashed roundy-rounder railfan type, geographic order takes a backseat to the vignettes I want to have. *If* I can organize them in roughly the right order, it's a bonus. Double-bonus word-score if the scenes are also oriented in the right direction.
Case in point...my planned expansion of the Juniata Division might have the Sherman's Creek bridge at Duncannon between Spruce Creek and Huntingdon. This is a nonsensical arrangement based on the real Pennsy Middle Division, but Duncannon is such a classic Pennsy scene (4-track interlocking on a stone bridge with the Susquehanna behind), it screams to be included in a section of the track plan that would otherwise be boring.
To me, the only real danger here is making adjacent scenes that might not fit. An example might be Horseshoe Curve leading directly into 30th Street Station.
I doubt any a$$hat would eat your lunch for including scenes out of order. As long as they are realistically executed, I think you're perfectly safe.