This is actually a bit awkward because the change was actually to make mystic shot proc first, so it procs stuff like bullet resist shredder, and then deal your increased bullet damage.
This is unfortunate because then the reverse isn't true as you mentioned.
I don't think there's a way to make them all work at once unless you specifically make spirit shredder bullets trigger on bullet hit, before any damage is dealt. But I feel like that can have netcode issues, or it might pierce stuff like Plated Armor, or who knows what else.