$5k for a topper seems way out of line, unless you got the one with the walk-in door, since I know that feature by itself is about a $1500 add-on. I'd definitely shop around a bit and maybe even look at dealers in another region of the country.
Mine was just under $2500. True it was a "lower end" basic cap (I specifically did NOT want an all glass door so buying the "cheapie" was the only way I could get an aluminum framed rear door) but I added on a few options: Side opening win-doors, carpeted head liner, and the built in tracks for the Yakima/Thule rack.
As far as the topper vs. no topper conundrum, it all comes down to how you use it.
Me, I've owned 6 pickups in the last 35 years and they all had toppers on them. But that's because I use my pickups the way you would use an SUV. I don't use it for work (I work in an office), I don't haul motorcycles, refrigerators, tractors, ATVs, etc. By contrast, I DO often carry things that need to be protected from weather and theft (camping gear, hunting gear, personal stuff, etc.) So for MY uses, a topper makes sense and there are no real downsides to it. On those rare occasions that I might want to haul a motorcycle or a bunch of furniture, it would make more sense for me to just go out and rent a trailer than to try and take the topper off so I could haul it in the bed.
OTOH, my step son has owned nothing but pickups since roughly 2005 and he has NEVER had a topper and never will. He uses the bed of his truck to haul lawn equipment and needs to be able to access the bed from the side, plus he needs to be able to put things in the bed that are taller than a topper. So for him, a topper would interfere with what he needs the truck to do.