The Eldar FAQ says nothing about Spirit Stones outside of Eldrad's entry. The Farseer FAQ you're looking at just says "What Mastery Level is a Farseer? Mastery Level 1." Honestly, I think at this point, where the codex has no ruling, you default to the BRB. Spirit Stones lets you cast 2 powers a turn, therefore he's Mastery 2.
On an unrelated note, I never noticed this until the FAQs, but the entry in the BRB on bikes says they just get straight +1 Toughness, and every single FAQ says to use the bracketed value for everything. Bikers just got insane at natural T5, and Nurgle Bikers just got terrifying.