Is it safe to use this tool on files in the Library folder? I ran it on my Library folder then remembered my Overwatch exported settings are in there. Will that affect them in any way?
And this is unrelated, but is it safe to run my .world files from installed worlds through it as well?

I wouldn't recommend using S3RC on anything but CC or when converting Store content- and even in those cases, I'd consider it a tool to only use when you know what you're doing specifically and not as a blanket sweep. Any advice out there to just run everything through it is irresponsible.

It's really not necessary, and worlds and lots have delicate links to all of the objects they need to function that can be severed by modifying the files in that way.