Auto rally does a rally attempt for all units at end turn. Why one would turn that preference to off eludes me, unless the user wants
everyone to rout off the map??
No units "take cover" automagically. "In cover" is
not a game status, its a
result of a voluntary action by the unit (by user or as a reaction to fire on it) which
may break LOS or
not. The user is
not informed if the LOS was broken, there is
no flag set (like for dug-in) - merely that in the dice rolling for the "take cover" function he may or may not succesfully break the enemy LOS on that unit. The success (if any) might be inferred if the enemy continues firing on him, as in real life.
SP3 had a "positioned" flag which units got if they stayed put for a turn(or 2?) which was a kinda-sorta 1/4 way to being dug in. And they may have become dug-in in 10 turns or something like that IIRC, but SP3 was a brigade level game where turns were 10 minutes or so.
In all earlier SP games and ours, you get to be "positioned" by halting for a whole turn. Its a very minor bonus. and applies if the "moving at x Mph" message is
not shown.