The installer will always install in all supported sim at once, that's another of the many advantages of the new installer. Before, if you wanted to install into two simulators, you had to run it twice.
Some reasons why the FSX choice is not available are:
- Your FSX version is not supported, for example if you haven't installed the two Service Packs.
- Your FSX registry keys are missing or pointing to the wrong folder.
- You used the P3D Migration Tool, so your FSX registry is wrong because is now pointing to P3D, but there's no P3D there.