If the pack order has Vanilla 3D above Fresh Animations, then the entity models included (skeletons, horse saddles, golems, etc.) would take precedent over Fresh Animations, making those entities have vanilla animations.
However, if you prefer Fresh Animations animations and models, then switching the order of the packs will reverse the priority, supplying the Fresh Animations models and animations instead of Vanilla 3D's.
Sadly, there is no middle ground with this pack's models and Fresh Animations animations, due to the way Optifine stores both models and animations in the same file. Hope this helps!