The argument is that an AE like fireball gets the bonus on each creature. A ray should likewise get it's bonus against each creature. If all rays are on one creature each ray should still get a bonus.It's ambiguous, and therefore up to the DM. Personally, I would regard a single spell as a single source of damage and use 4d6 + mod. Otoh given that each ray has an individual miss chance it would not be unreasonable to add the mod to each ray. The flipside to that is that resistance would also apply to each ray individually. Choose wisely.
Wouldn't resistance have the same effect regardless?
.