The usual solution to avoid embedded seam allowances is pieces of cardboard that slip under each edge/facing. The silly things don’t stay in place when you flip the garment right side up (unless you have prehensile toes to add to the equation), so combining the parts is an elegant solution.

Key the closed top of the zip with a chalk line (washable marker?) before you start inserting. When everything’s sewn, the lines on each tape should match perfectly. The couture version is a hand-basted thread that runs across and is then clipped, ooh la la.