See: other thread regarding RWG maps missing traders. If they're missing traders, it's pretty easy to imagine them missing Duke and Noah's compounds, too. Roll a RWG map and you don't know what you're going get, POIs and otherwise. Some I haven't seen since A21. That's why I wouldn't want to wrestle with it were I TFP.
That's different, depending on exactly what they do.
First, traders have limits on how close they can be in RWG. If there is no room to place one because it would be too close, RWG likely will not place it (I don't know if it overrides those for any reason). Second, traders can only be placed on gateway tiles. This limits availability for them to be placed. Third, traders need a town to get placed and towns in RWG can't cross biome boundaries, so if a small map makes it where a biome has no space for a town because that biome happens to be filled with mountains or rivers/lake stamps, then there's no place for a trader.
Now, look at any specific story POI. They can make it so those can appear in all biomes if they want. They can make those use a very common POI size so they have many more places to appear. They can make those appear in all districts so there are many more places for them to appear. They can make those a priority in placement - place them before other POI to guarantee they are placed. And if they feel that still has a chance of not placing them, they can make them wilderness POI instead of town POI. Wilderness POI have no restrictions other than terrain or not being too close to a town. That means they can easily start wilderness POI placement by placing those required POI and since RWG always makes maps with a lot of flat or "flat enough" terrain for a lot of wilderness POI, there's really no chance of them not getting placed.
And that's all without them needing to change RWG at all to guarantee that they are placed, which they could choose to do if they want.
As far as POI you haven't seen, some POI were removed and/or redone in 1.0. Some of those that were redone don't really look the same as they were in A21 and may not be recognized if you aren't reading the POI names and remember them from A21. That's not related to RWG POI placement at all. There was a "bug" recently that limited placement of certain tile types, like caps, that made it very difficult to ever see certain POI that have very limited placement options, but that should be fixed in 2.6.