The point is that you can change the starting skills at level 9 with restarts, and Expert Summoning greatly simplifies the start. Darkness isn't mandatory in this mission, but it will be very difficult without it in subsequent missions. You can take the skill without Darkness itself.
It seems that a Phoenix is needed, and I didn't get it in the first mission, so it makes sense to take the Tome of Summoning Magic as a bonus at the beginning of the second mission, presumably for those who also don't have the Phoenix Summon skill.