DisplayFusion does run 64-bit. It installs to Program Files (x86) just for compatibility reasons, but the process runs 64-bit. You can verify in Task Manager. In Windows 7, it will show a * beside it if it's 32-bit, and in Windows 8/10, it will show (32 bit).
It should really install on it's correct folder. The whole purpose of the 2 folders is to separate the 2 types. I would think Windows supports the 2 folders.
For compability it sounds more like a workaround, since there are many types of system and OS variables that can be used to properly use the path.
