Just going by what has always worked for me. I've been installing games and mods into my Program Files folders for probably 15 years now. I've never had a problem with mods in any game, and I always ignore all the warnings about not putting stuff into Program Files because it's just nonsense that started with Vista and it's overzealous UAC. There are no good reasons to not install games or mods in there. Steam installs to Program Files by default. All my games are in there, SH3 Commander is in there, my other mod utilities for other games are in there, all work without a hitch. Don't even need to run any compatibility modes, except for sh3.exe.
As long as UAC is off and you have admin rights, there won't be any problems.
I understand why mod developers put in the warnings on their installers, because not everybody knows about UAC or how to turn it off.
I just think people should know that installing games into your Program Files folders is not an issue. I see far too many baseless warnings against it.
As far as other warnings are concerned, I would never tell anyone to ignore them.
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