Oh, now i remembered, in my near full game, i had like 13-15 spirit, some of them actually getting from runes that decrease max hp, but increase spirit by one
So, notably this isn't possible on hard mode (you can't go over 3 starting spirit) and can only be taken once from Sophia. There's also the runes, as you mentioned, Vili's Wisdom perk, the teachers pet perk, three levels of "spiritual reserves" perk from levelup, and the nymph's blessing. Most of these (Vili, Sophia, and Teachers Pet) all have negatives, but are fairly easy to mitigate.