I'll take a shot at answering your question, even though I'm just a novice compared to others on FRF.
I believe the ride may be based on what you previously had before. In my case, I went from a Honda Civic Hybrid to a Raptor, (just a minor change in gas mileage, 51 to 15 mpg). The Honda was smooth on the highway, but if I hit a pothole, the car would "bang" so hard, I often thought I broke something. That same pothole for the Raptor would hardly be noticed. So it's really part of the design of the suspension.
Also, I have a coworker who has an F150 Lightning w/ ecoboost and we were comparing the two. His Lightning was designed for comfort and has a very smooth ride. On base, we both drive the same road, and there is a section that is rough payment. I can feel this in my Raptor, but not in his Lightning. Therefore, I believe what you are feeling is by design. Would I trade my Raptor for a Lightning, absolutely not. BTW, he only gets 15mpg on his ecoboost, so I am very happy with my 6.2.
I think you have an excellent buying opportunity there. I've seen a few low mileage Raptors for sale (when I bought mine). Some people just don't like its features which are designed for a specific target market. You just need to ask yourself if you will treasure your Raptor like I do. I just know this will be the last vehicle I own, and perhaps 20 years from now, when I can't drive anymore, I could see my well maintained 2014 SE being auctioned at Mecums. A Lightning probably not.
BTW, I agree with the idea of a full inspection. I did see a used one for sale at a VW dealership that had been trashed by it's former owner. However, I've also seen a brand new Ruby Red SE for sale on EBay if you prefer new.
