Windows – the difference between “Program Files” and “Program Files X86”

I searched on my own (well, I should have done that earlier) in the Apple Support Communities and I found this and this thread. It seems that there is no 64-bit version. The simplest explanation is:

There is no 64 bit iTunes. The 64 bit installer installs 64 bit drivers but 32 bit itunes.

From the Windows perspective there will be no side effects or configuration problems, unless you have a folder with the exact same name in that location as this will cause you to overwrite that folder.

From the third party applications perspective it depends on how the application is written to check the folders, but this is very unlikely to occur and it is not a problem that causes your system to fail.

It is best to keep them separated but if you really can't do it then go ahead, your system will not die...