Whelp, that didn't take much experimenting. I started with a brand new fresh install of SPT 3.6.1 and began by only installing the Game Panel HUD mod by itself. All exfil locations and every other setting were functioning perfectly. My mission to begin installing one mod at a time and checking to ensure the compass was still working ended after only installing one more mod, which was the KMC Server Value Modifier (SVM) mod. I went into Woods and still had the Crossroads exfil show in my compass, but my other exfil locations were completely missing.
At this juncture I'm just going to chalk it up to this mod does not get along with various other mods in it's current state (a few people have already pointed out Helicrash), and hope that an update from the creator may fix it someday.