That’s how it is in reality. When there are no VORs between airports or IFR waypoints, whether it be low or high level, there is nothing to make it up. Highly probable between airports that are very close to each other or regional or even smaller airports.
Also that there is no tower communication is probably because of the fact that the airport has no active tower. In aviation this is called UNICOM frequency. At least that is what I assume is causing your observation.
Maybe you can provide an example route you were referring to before doing a lot of work to fix it and so that I can confirm.