Mostly as far as the windows and badge contributions work.
The tricolors require more badges(compared to the regular waypoints in that stage), but give more points. The tricolors allow you to switch to a different path if you like. Ex: you could go blue path only thru the 2nd blue tricolor, then complete the orange tricolor and continue to the flag on the orange waypoints. This would skip the orange waypoints up to the 2nd orange tricolor and skip the last 3 blue waypoints.
This allows a strategy of skipping some waypoints that have badges that are harder for an FS to make. Small city FS's may have a really hard time making certain badges, and depending on where the bulk of those badges are required, they could plan a way to the flag skipping from one path to the other as they see fit. Any strategy that gets you to the flag gets the prizes for that stage.