You could put tiles in the UFO which only show up on crash sites, and are recovered for points. Thus, skipping the crash site removes the opportunity to collect the points.
It takes some advanced level modding, but if you're determined to do it, then get some baseline experience with Volutar's mcdEdit and hit me up on Discord or here for details. Discord is a much faster way to reach me; I am thereaverofdarkness#2362. On the other hand, if you are already an advanced modder, then you can simply peek into my mod Reaver's Harmony and see the method based on how I have done the Data Capsule items.