In the "Gafgarion fight" where you have to pull a lever to open the gate and let your party join Ramza is at the Gates of Lionel Castle; here a character can be up on the wall with another character underneath on the path through the gates. And Inside Igros Castle, (SPOILER)where you fight Dycedarg with help from Zalbag, I believe there is a bridge that you can stand under while another character is on the bridge above...and I'm sure you can be on and under the bridge at Zirekile Falls. Those are the storyline battles that I know of where it is possible.
Then there are the extra missions like Nelveska Temple where you can be on the hill and underneath it inside Worker 7-New's cave. As well as (I think) the first two battles in the Colliery Underground, where some Chemists and Behemoths hide in doorways and caves. Is that all of them? :fpcurious :fphigh: