Programs that runs on "Program Files(x86)" use the WOW64 framework(a set of drivers and APIs intented to run x32 applications over a x64 architecture system):

The WoW64 subsystem comprises a lightweight compatibility layer that has similar interfaces on all 64-bit versions of Windows. It aims to create a 32-bit environment that provides the interfaces required to run unmodified 32-bit Windows applications on a 64-bit system. Technically, WoW64 is implemented using three dynamic-link libraries (DLLs):

• Wow64.dll, the core interface to the Windows NT kernel that translates between 32-bit and 64-bit calls, including pointer and call stack manipulations
• Wow64win.dll, which provides the appropriate entry-points for 32-bit applications
• Wow64cpu.dll, which takes care of switching the processor from 32-bit to 64-bit mode

64 bits system need to "emulate" 32 bits applications, that is the reason why two program files folders are needed.

Programs that runs on "Program Files(x86)" use the WOW64 subsystem (Windows 32-bit on Windows 64-bit is a set of drivers and APIs intented to run x32 applications over a x64 architecture system):

The WoW64 subsystem comprises a lightweight compatibility layer that has similar interfaces on all 64-bit versions of Windows. It aims to create a 32-bit environment that provides the interfaces required to run unmodified 32-bit Windows applications on a 64-bit system. Technically, WoW64 is implemented using three dynamic-link libraries (DLLs):

• Wow64.dll, the core interface to the Windows NT kernel that translates between 32-bit and 64-bit calls, including pointer and call stack manipulations
• Wow64win.dll, which provides the appropriate entry-points for 32-bit applications
• Wow64cpu.dll, which takes care of switching the processor from 32-bit to 64-bit mode

64 bits system need to "emulate" 32 bits applications, that is the reason why Windows need to "segregate" two Program Files folders.