There's no law against taking your shots on film, scanning them, and using the available software to do a combination.

Bear in mind that when you refocus with the lens, you will get small changes in perspective & magnification- the distance between the front element and your subject is changing. This could be important when you are focusing so closely. The software is probably correcting for that as well as doing the simpler image combination.

But personally I think front-to-back sharpness is far overrated. Why not use the out-of-focus transitions to convey dimension, and use tilts to place the plane of focus wherever you wish.