It simply depends how the other mod is made. The NPCs of pure roleplay encounters are mostly in a neutral faction so there should be no problems. For the other ones it's completely ok and planned if for example my legion slave caravan gets slaughtered by mod added NCRs/Creatures and the enslaved NCR recruit is freed by them. The slave is pretty good in hiding and running if set free as I could test shortly. This guy survived scorpion valley (respect). And in the legion play through he ends where he belongs... in the slave pen
if his guards survive.
You see I try to take care of all possibilities .
If a location that I have chosen is already overrun by critters that another mod adds, still no problem. It's a !!! random !!! encounter mod. The encounters are designed in a way that they can happen everywhere. If one ends in death then it simply does it. If the sleepy prospector decides to sleep nearby mod added Radscorpions then he made this bad decision and still it's funny to watch how the little bed bugs try to fight the scorpions after his poisoned death.
Maybe you see how the story ends in another play through at another location if it's a unique one. The repeatable ones can be seen in the same play through again because they are repeatable.
So no need to worry except your whole Wasteland is overrun by insane Deathclaws
.