More Commands in Battle

According to what I've seen in the event log, Gogo's command list is added with the bit that checks you've obtained that character (in other words your first conclusion).

As the sub menu, I sure couldn't pull it off at this time.
As for starting with the cursor in the sub menu, I think I pulled that off by mistake once or twice so it should be possible.
As for command relics, I'm not sure that would be practical to accomplish since it only replaces a command on a character by character basis. At this point the characters wouldnt have skills like Fight or Magic in their own list so... the best I'd hope for is making the items replace other character specific skills (like mug and gp rain).

I definatly will not say not possible, but I personally didnt find great documentaion regarding battle windows.