Hi Joshua,
Thank you for such a thorough explanation of your issues. This is 1 million times better than the usual “it’s not working”.
We may have to hold this up as an example to others as a really effective way to describe the issue.
I doth my cap to you sir.
Now onto your actual issue.
What I am seeing is expected behaviour on how the Gradient tool works.
This will project a plane from the point you click -> drag and fill the gradient based on your settings (it’s actually perpendicular to the view where you click – if that makes sense).
In this mode, anything on the positive side of the the projection plane will be affected.
To see this in action, click in the middle or model and then drag in any direction, you will see this perfect line where the gradient starts.
There is a radial mode which emits a sphere from the point you click, but that is based in view space so will affect everything under cursor regardless of the distance (ie – it will always project through to the other side)
In simple terms – The gradient tool isn’t useful for what you are trying to do.
Fun Fact, I’m actually trying to rework that radial mode to be in world space which will mean it won’t always project through to the other side of the mesh and will stay purely where you click.