This can be applied to any game. I have not tested this out so it’s probably extremely inbalanced. The free-deployment option lets you place the # of units of each class (infantry, armored, sub, tac, etc.) your country starts off with anywhere you want in your starting territories.
If you are placing navies they have to be in the areas where the historical game deployment are at. This means you cannot as Germany just place all your subs off the coast of America, but you can stack all of them in 1 seazone instead of having them spread out like the historical deployment. You basically can choose whether to put units in the starting territories or not.
Since I am more familiar with G40: Axis deploy first, Allies second. This makes it so the allies can place their units in response to the Axis initial placement, making it more balanced for the Allies.
Other versions of the game you will have to experiment. It may be better for both parties to place their units at the same time.