If an alliance fails to toggle the flags of the opposing alliance, (switching them to their color) does the opposing alliance receive credit for these flags, even though they may have started with their color facing outward?
The only thing that matters is which directions the flags are facing at the end of the match (or autonomous). It doesn’t matter if they ever moved, or who moved them.
Thank you. I am assuming this is the same for the caps too?
Yes. Even objects scored by breaking the rules will be scored as they rest at the end of the match. However, the referees will be looking at if the illegally scored objects affected the outcome of the match for determining if a DQ should be given to the offending robot(s).