We tested this actually, myself and a clan that were matched up that knew each other. From our own testing, we saw champions using their assigned AI and skill order, not the default.

So that's one thing working as intended, at least. :)

If you want to make any AI changes you have to do it from the arena saved teams menu.

Siege just copies whatever is there.

Yup. Every time I set a defence for the first time and employ a preset the "team setup" button lights up blue like it does in arena to indicate that a team preset has been selected; but then when I go back in to edit the team the "team preset" button is back to its regular color indicating that the preset has been deselected. I've also seen some wonky AI in enemy teams, like Mikage not transforming or Armanz not using his A2. I'm certain presets don't work in siege.