All this shows the biggest advantage of human player vs. AI: the latter cannot plan ahead. Looking at those command oddities I come to think that the only thing AI focuses on is the chance of winning the battle here and now - without counting in the consequences of eventual defeat or retreat. Thus, AI gets notoriously oblivious of the fact that abandoning the province now may make it royally difficult to reclaim at a later date. Not to mention retreating into the puny fort, where the rest of the army simply has nowhere to go, and the 'lucky' 200 men who have escaped instant capture would last only a year or so... I would consider it a waste if all the best units in my army (sometimes with an heir or other good figure) got crammed into the fort and starved, whereas the rest (say, 400 peasants or spearmen or some other low-level rabble) retreated into neighbouring province - with no effective chance of mounting a successful counterattack. The problem is, the AI considers it perfectly viable. Oh well...
As far as excommunications go, I cannot tell of any serious deviations from the general rule - if you are significantly stronger (say, twice the provinces and/or army) and attack, you get warned, then excommed. Following this rule, The French can exchange blows with The English all the way they like, and the Pope doesn't even sigh as long as things look at least remotely even. Just you wait until your armies begin to trample some smaller buddy (like Aragonese for example, as they like to backstab you every now and then), and the moment later you hear the old crone screech from his sandcastle: "In the name of God, repent, or else...". Yeah, right, old man, just sit tight and don't make noise.
Well, maybe for the French it is not that wise to mess with the Pope after all, since most of their GA are associated with crusading. Thus, in my recent French campaign, I obey and adhere to every single word from the Papal Capital - which in turn blesses me every two years or so with a grand of gold. Not that bad of a cooperation, after all