EDIT: Code is no longer relevant (that wasn’t the issue). My issue was with Half-Pixel / Texel issues in a pixel perfect game. Since using the new shader all issues are fixed. See accepted answer for the links to the shader.
NOTE: I have not tested this using OpenGL yet. I imagine a regular sprite shader would be used in that case.
It turns out a ton of my issues were related to half-pixel / texel issues. Everything was solved by changing my texture atlas shader to Sprites/Pixel Snap/Alpha Blended. So happy to have a easy, clean fix finally.
You can download the shader here, from my Google Drive.
Here is where I found the solution.
Here is a direct link from Unity if you don’t feel comfortable download from my drive. This contains a large collection of shaders and not just the Sprites/Pixel Snap/Alpha Blended.
I’ve also [23053-sprites-pixelsnap-alphablended.zip|23053] the shader to this post.
Hope I can save some people some trouble.