The cleanup of joins between walls in the main model and walls in the primary option works the same way as when all walls are in the main model. To avoid incorrect wall joins between the main model and secondary options, move the wall from the main model to the design option set. See Moving Elements from the Main Model to a Design Option....
Walls in the main model
A wall added in the primary option; join cleans up properly
A wall in a secondary option joined to the main model
To avoid the above problem with wall joins in a secondary option, add the horizontal wall to that option. The wall join then cleans up properly, as shown. See Working with Wall Joins.
