Not really, see you just said, you needed to go in and set that parameter, I don't have to. but you have to every time.
It does not work like you assume. Each time you create a new toolpath you need define its parameters no matter which software you use... right?
Mastercam has a tab called "linking parameters" within nearly all toolpaths. This is where you set the depth of the feature, top of stock for that feature, tool retract height and clearance height.
You can leave these as defaults if you want, or you can go back into the tool path parameters and change them however you'd like, it only takes 3 or 4 mouse clicks.