I am aware that when a shugenja attains a new school rank they can choose spells of any mastery level they're allowed to cast, but I couldn't find anything in the rules stating one way or another whether a shugenja starts with all master level 1 spells, or if they can choose master level 2 spells for their affinity element.
There is an example on page 163 of a rank 1 shugenja casting a level 2 spell:
EXAMPLE: Lucas’s character Isawa Butaro is casting Fires from Within, a Mastery Level 2 spell. Butaro is a Rank 1 Isawa Shugenja, and has Fire 3. He rolls 4k3 (4 = Fire 3 + Rank 1, keeping Fire) against TN 15 (5 + ML 2 x 5). He rolls a 2, 4, 7, and 8, keeping the 4, 7, and 8 for a total of 19. The spell has been cast successfully.
However, I don't find this entirely conclusive because it's possible the shugenja found/gained the scroll for Fires from Within after character creation.