However, consider this: things will change.
You may end up "re-sanding/re-surfacing" or otherwise needing to refinish the mouse section.
Make the issue moot. Leave the desk area alone. Make the desk consistent and just find and use some mat or other surface upon which to use your mouse.
Simpler. Provides more flexibility. (Imagine a guest who is left-handed and your mouse "surface" is on the right....)
So, if anything, go with an interchangeable mouse pad but not one embedded in the desktop.
Leaves you free to make whatever mat you wish and experiment accordingly.