So I decided to verify some levels of jug pets since the update notes said beast affinity would apply over level 99. Turns out nope full beast affinity merits same hp as one called without any merits.
The update notes also said "If over level 99: Main weapon item level + the pet’s maximum level" but calling a pet with brethen axe of ilvl of 113 my pet had exactly the same hp as without.
Only when I had a weapon with ilvl higher than AND beast affinity merits did it's hp go up ie did it gain ilvls.
Beast affinity merits raise the maximum level of a jug pet so according to the update notes that alone should raise the pet above level 99 and also according to the update notes just changing weapons should as well and "If over level 99: Main weapon item level + the pet’s maximum level" they should add together but instead it takes whichever one of those is the lowest.
This sounds like a bug because of the notes and because all the other pet jobs merely put on 1 item and their pets are now much stronger. A dragoon for example would have a level 120 pet I beleive with delve polearm. While bst right now has to equip said ilvl weapon AND put merits into beast affinity AND make af2+2 AND augment it and even with all that the pet would still be stuck at ilvl 114. So if this is intended it is very unbalanced and should be fixed anyways