I have worked on many Lugers, military and civilian, and I have owned probably a couple of dozen at one time or another, ranging from first year of production to the end of WWII. Maybe some guns were hand fitted, but I never saw any that appeared to be. With only a few exceptions, parts appeared to fit and interchanged, whether taken from guns or spare parts. (Not all ammo functioned the guns, but that is not the same as saying parts did not fit.
That does not mean that there might not be problems, but I can only say that, for the most part, the Lugers I worked on were properly fitted and that seemed ti be the result of careful parts manufacture, not of any extensive hand filing or fitting during assembly.
Apparently, Luger (and P.38) parts were numbered for one simple reason that probably made more sense to the Germans than to us - they had always done it that way. And no one ever questioned it, even though the practice slowed production even in the most critical times.