Alright so after a two week break from game dev I came back to test some more of my code and try to get to the bottom of this (sorry about my frustrations the other week I was rushing myself for no reason and got really impatient). After further testing I was able to stop the infinite scaling/additive from being applied every frame by putting setToSetupPose outside the IF statement(in PhysicsProcess) like you suggested. I had already done this earlier in the thread but I probably should have specified in my previous post that while it fixed the scaling issue it brought a few new problems with it as it wasn't a perfect solution.
Because this is a recoil animation, I need this animation to be over very quickly, which means no mixing when adding/setting the animation and only a very small amount of mixing when mixing out (currently I'm mixing out using two empty animation tracks. However when I have the mixduration (or delay, they both seem to have the same problem) on the Add/SetEmptyAnimation set to a very small number say below 0.5, the animation seems to rapidly transition between the two states (seems like every frame) and it seems to do this for about half second before resetting to normal. I could try using godot's timers instead of mixduration/delay since it doesn't seem to be working properly when both the add recoil/add empty track logic is in the same IF statement. Is there something else I should be doing for mixing out the recoil in this situation?
The second problem is that my aiming logic is completely invalidated by the setToSetupPose being processed every frame, which is uh, kinda a big problem for a twin stick shooter. The projectiles are only being shot from 1 angle (which is flipped if you're looking left). I tried using both a SpineSlotNode and SpineBoneNode (they both work the same for aiming projectiles since you're simply taking their rotation and position) and they both produce the same result. I would think the aiming be limited to at least 2 angles depending on if you're looking down or up (front and back view have different aiming animations). Any ideas how both of these problems might be alleviated while still having the ability to have additive recoil animations?
This is what I have for code atm 
and here's a small clip of what's happening (the rapid switching is a lot less pronounced in the clip probably because of the low frame rate the vid is set to)
