It seems only the military rifles cannot be altered.
It applies to all firearms that are less than 50 years of age and have been added by ATF to the C&R List. It is just that few handguns are modified from their original configuration because of their value.
You can put a new stock on a 1903 because it is a C&R by virtue of its age. A new stock will not change that. The catch is
imported firearms. Per the 1968 CGA, the only legal way to import military firearms for civilians is if ATF classifies them as C&R. It doesn't matter if it is older than 50 years or not, the reason it is allowed to be imported is because ATF says that it is a C&R in its original, military configuration.
The prime example is the SKS. In its military configuration, it can be imported into the US. If you make alterations to the SKS, it can lose its C&R status, which can put you in violation of 922(r), which prohibits the assemply of firearms from parts which would make a firearm illegal for importation.
Most of these people that buy a SKS and slap on a pistol grip stock and a 30-round magazine are violating the law, they just don't know it. As most gun fanatics know, you can do ATF's "parts count" game and get around 922(r). The average Joe Blow doesn't know that.
Of course, there are exceptions to the rule. The Chinese Norinco SKS imported prior to 1989 is exempt from 922(r). The Post-89 Norincos were imported without bayonets because ATF ruled them "sporting" firearms in that configuration. Adding a bayonet puts them in violation of 922(r).
And yet, I am not aware of any incident of anyone being charged with modifying a SKS in violation of 922(r), so why worry about it.