@fsecco, the graveyard order and game layout are treated similarly. While you are correct that MTR section 3.14 says that graveyards using cards prior to Urza's Saga can't be reordered, most decks in Legacy and Vintage don't play cards that are affected by graveyard order, so judges won't strictly enforce it. If a player is playing cards that are affected by graveyard order, they must keep their graveyard in the proper order.
The same thing goes with board layout. As long as it's clear to all players, anyone playing a deck that relies heavily on the graveyard or exile may expand those zones.
If the setup of the game causes some confusion, the judge may issue a warning for Communication Policy Violation and could back the game up to the point of the decision that was made based on the incorrect information per IPG 3.7.