The program that you bake in does matter to a degree since:
- It must fit nicely into your production pipeline/workflow
- If you are baking tangent based normal maps then the texture baker needs to use the same tangent-basis as the software that will be rendering it in the end.
Up until a few years ago, there was no standard for the tangent basis. It was a wild west where different programs would use different math (and in some cases, programs like 3dsMax would even calculate it differently depending on if it was baking or rendering). A normal map that looked right in one program might look wrong in another program, leading people to think their map was baked wrong. Nowadays a lot of programs and engines seem to be settling on using Mikk, but that’s not always the case. One of the reasons I prefer baking in Xnormal is because it will let you change which tangent basis is used so that you can sync it to whatever the renderer/shader is using.
I don’t like baking in zbrush because
- You can't use meshes with differently topology (which also means you can use tricks like floating geometry)
- There's no way to specify the tangent basis being used
- There's no way to control the vertex normals (something else you'll usually wan to have synced between the baking and rendering process)
Also I assume both meshes (low and high poly) must have same UV’s.
Only the low-resolution mesh requires UVs.