I just finished gluing the stringer and the foam blanks together, it is not perfectly aligned.
The glue up simply holds the blank together so you can shape it. An uneven glue up will just be a little more shaping to level everything out. Glassing the board provides all the strength and the glue is not really a factor in the board.
If you have space between the foam and stringer you can squeeze more glue in. It will expand to fill the gap and is shapeable.