Ok, what's probably happening is that the characters have common files that they use. Content creators often do this. The character files, usually pz2 files in the pose menu for these type of v4 based characters, are only the tip of the iceberg and there will be other files that support them. The content creator will not make new different files for example for blue eye textures each time. While some put each characters files in different named folders other simply use a common named folder, such as FredBloggs/eye textures.

So that every character works, these common files are included with all figures. So when you copy a second runtime into the first your operating system ( Windows or Mac) will detect the files are already there and give you the options.

It doesn't really matter whether you skip or overwrite these files, I usually overwrite if I'm installing a more recent runtime in case there have been any minor updates. I wouldn't recommend keeping both files in the runtime as this will only bloat it for no benefit.