Thats a first!!!! Congrats
Considering 3.0 might as well just be 2.7, it's not really a first. It may be considered to be a major update, but it's really just turning XML modding into game options. Yes, I know there are changes to make those settings work better, but even though this will be a "big" update in that it will make for significant changes being possible in vanilla for how the game plays, it won't really be what we normally consider a major update and only major updates (usually) required a new save.
@faatal This happens often with wilderness POIs when too close to roads. Couldn't there be a buffer zone around wilderness POIs to keep them from spawning too close to roads? (obviously, this question is posted by someone who knows nothing about programming

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Was the issue fixed where certain very large POIs don't spawn anywhere on the map?
The short answer is yes. Teragon has a parameter you can change for roads that will make roads more or less "detailed" in where they are placed so you can avoid this issue. The drawback is that road generation takes longer, the more "detailed" you make it. Teragon calls it simplification. Basically what is means is that with no simplification, the road generation uses the full size map, which allows roads to avoid POI without a problem, but takes longer. As you increase the simplification number, the map size being used is cut in half for each increase in number. So 1 would be half the map size, 2 would be a quarter the map size. This speeds processing up significantly, but it does mean that the location of a POI isn't as "precise" because of the reduced map size. I admit to not having looked too closely into how it works, but I think I'm correct that if a POI covers a block at 1,1 and you are using a full size map, it's known that it's at 1,1 but if it's a half size map, that 1,1 would be seen as being at 0.5,0.5 meaning the real location could be 0,0 or 1,1 or 0,1 or 1,0. And that's just at half size. That makes it more difficult to place roads around the POI since you're not as certain of where it is.
Now, RWG may not do things that same way, but as Teragon can avoid the issue entirely at 0 simplification, it shows that it is possible to avoid it with the road generation. I can't say how best to manage that, though. It may be a buffer, though you of course must have a road that connects to the POI if the POI has a driveway, so you can't entirely keep roads away. But you could place a buffer of X for any road not connecting to that POI and then set it so roads have to come in straight to the driveway from a distance of X, which when combined with the buffer would keep the roads from cutting into the POI.