Well, I have had a 24’ x 12’ arbor for the last 10 years and understand the issues that you are dealing with -
Are you spur pruning or cane pruning off of the cordon?
You would be pruning in order to choose and train the shoots to follow the cross pieces. Any chosen shoots that tend to grow opposite would need to be bent to grow the direction desired.
Actually I think that it would be best (based on my experience) to have the trunk up one of the legs and have the cordon diagonally thru the middle of the pergola to the opposite corner.
In any design that you choose your always are going to have shoots that run off of your pergola. Get used to that. I just let them hang and not worry about it.
You have a lot of options.