I gotta give the nod to the commercial action. Within reason. I like the idea of a clean sporter action with all the work done. But just about all of the aftermarket goodies are geared for the military action.
Many commercial actions differ length between screw holes and have their own style of bottom metal, many also use aluminum. The way the trigger attaches may differ also, but I don't recall at this moment.
I would decide what I want the finished rifle to look like and verify that the parts are available for the action you are looking at. If you are buying a complete rifle, just treat it like any used, obsolete rifle.