There are at least 3 ways to ensure that a printed part is made large enough so that a subtractive operation can then mill it to "net shape".
Scale in CAD
You can scale the model in CAD, export to Simplify3D, then suppress the scaling operation before generating subtractive toolpaths. This will not work annular features such as center-holes, which would also increase in size during a scaling operation, resulting in less material rather than more.
Scale in Slicer
You can scale the model directly in Simplify3D. This has the same limitation as above, where it could cause a reduction of material rather than an increase.
The safest, most efficient, and most controlled method is to create a separate model for printing. This gives you material exactly where you need it, none where you don't, and you can remove unneeded detail for faster printing. This is the recommended method.