This is something you should never do. If you do, and you disconnect the hard drive with the System Reserved partition (which might not be the OS drive), then you might not be able to boot Windows (though, as you said, it can be somewhat easily fixed).
If you have multiple hard drives in a computer, before you install Windows, you should make sure every hard drive (other than the one you want to install Windows on) is either disconnected, or has a complete partition on it (using all the space available on the hard drive). That way, Windows setup won't place the System Reserved partition on the actual first hard drive it recognizes.
Should note, for the partitions, they need to be created outside of the Windows Installer (since the System Reserved will still be created on a blank, first drive). This can be done if you already have Windows installed (and are planning to just do a clean install), or use a program such as GParted that allows you to create and edit partitions outside of the Windows OS.
As long as all Windows partitions (Recovery, System Reserved, and C drive) are on one hard drive, you should be good.