That's how WinSCP works. Note that the binaries in installer and postable package are identical. What makes the difference is that installer configures WinSCP to use registry (the default is not ise INI file).

When you start the standalone portable executable WinSCP.exe for the first time on a machine that has already WinSCP installed using the installation package, the Configuration storage will point to the Windows registry.

Not sure whether this is intended or a bug. This might be confusing at least...