Especially with Emissary, that interaction is actually not literal to the wording. As Emissary says "whenever faith is gained by another follower, gain 1 faith", which suggests that the Emissary is the one gaining faith (and thus should trigger Raven again). So as you've intended, the Emissary's wording should change to "when another follower gains faith, that amount is increased by 1". Although personally I'd recommend Emissary to be its own instance and trigger Raven an extra time since it's sort of a really subpar unit as long as Supplicant isn't nerfed and also doesn't scale well in general.
Overall though, I'd probably carefully recommend to make separate instances their own triggers. As it stands, triggers are unintuitive and also don't prevent abuse, as one effect still works while just one or two others don't. It's just a knowledge check, plus a bit more RNG involved.
On top of that the units in question don't really scale as well. They are harder to scale multiplicatively than just a stat-based strategy and they don't scale at all with stats gained inbetween rounds. Compare that to an Adaptive Familiar next to another Adaptive unit together with some permabuffs and you can easily gain +8+8 per round or more.
Ultimately, as far as balancing concerns go, I think you might actually be able to achieve the opposite with some clever wording. In permitting multiple triggers by default, you can then easily nerf overtuned units by making those triggers happen only "once per attack", or instead of being two separate effects, you can make the second effect increase the value of the first one, etc.
On endless, I also just noticed another soft-nerf option, which would be to put most of the special units in one of the first two spots so countered builds have the chance to kill them quickly. Except the Barricade, which should obviously be further towards the end.