JAE - that is not exactly how I think about it. Essentially you have ASCE 7 mandated over strength requirements for all types of systems and materials, and then you have the material-specific over strength requirements.
The two ASCE 7 sections I pointed out are applicable to wood, concrete, etc. as well as steel. Note that though it is in the 12.3 diaphragm section, 12.3.3.3 actually applies the overstrength factor to the beams and columns of the system.
For R=3 steel systems, it just so happens that there are no ADDITIONAL overstrength factors in the material code (AISC 360), while for other types of steel systems with higher R factors there ARE additional overstrength factors in the material code (AISC 341).
Since the O.P. asked about R=3 systems, I kept the answer related specifically to those systems, but there are other ASCE 7 mandated overstrengths that are not specifically related to the material as well, such as for example foundations for Cantilever Column Systems in 12.2.5.2.
One minor note to your post as well is that you can certainly use an R=3 system in SDC A, but in that case overstrength factors never come into play.