My two cents...
Normally the folders inside Program Files and Program Files (x86) and all files inside them are created by Windows Installer with specific access rights like TrustedInstaller or System and should not be directly changed by user; ordinal User account doesn't have enough rights to create/copy or otherwise modify these parts of OS. It's a kind of protection against some malware or wrong manual actions of non-professional user. If you use the software which doesn't have any installer, like simple utilities or portable versions, it's supposed to install (copy) it elsewhere, like to a folder in %userprofle% or on any non-OS internal or external drive.
From my practice, however, I use specific areas for such files inside both Program Files and Program Files (x86), although it's not recommended for typical user. They are Program Files\OS and Program Files (x86)\Tools (I use these names by historical reasons). Both have Administrator rights (ownership and full control access) and I can copy, modify or delete the files inside as Administrator (note that User still doesn't have full control rights there). Tools is used for many 32-bit utilities like Rufus, Tcpview, Dosbox, Testdisk etc, while OS is used for a few 64-bit utilities like CPU-Z, Process Explorer, Process Monitor.