The tracker is always initialized, regardless whether its input is used or not. This might change in a future version to enhance interoperability with Opentrack/Freetrack, but isn’t 100% decided yet because of possible unwanted side effects.
I’ve heard from several people that they where able use various racing titles with Opentrack/Freetrack the way you tried, not sure though whether there currently is a workaround for FSX.
You can get normal Rift headtracking by using FSX’s freelook mode, which is activated with [SHIFT]O per default (might be different for your setup though).
Hope that hepls.