JDBB When you turn an attachment into a mesh, where is this mesh vertex data stored?
What do you mean by "when you turn an attachment into a mesh", do you mean in the Spine Editor?
If you want to know whether mesh attachments directly store atlas texture coordinates: no, they store coords relative to the atlas region boundaries, and the atlas regions are defined by the atlas. Thus the atlas layout can be different and mesh attachments still work fine.
JDBB If I were to export a set of lower resolution sprites into an atlas using the spine texture packer, then manually load the low res atlas in unity and assign it to the skeleton data (that was exported with the high res atlas), would this break any animations that rely on having mesh attachments?
It does not break anything.