This is absolutely not true. FS9 can be installed ANYWHERE and still work properly. It can be installed on a different hard drive, external drive, flash drive, or SSD drive. In fact, the Program Files location is the WORST place it could end up, due to permissions issues in Windows.
Also, it doesn't matter if your program is 32 bit or 64 bit. Windows is smart enough to know what it is and how to install and run it.