it all comes down to what you plan for your truck.
for me I ordered my truck as seen in my signature because I already planned out my build before I ordered the truck.
Basically this is how I envisioned it before I ordered it.
Therefore, I only ordered it with what I have in my signature.
Can you add bed utility group (basically bed rail + LED light) later? Sure you can. Which is what I did aside from the light is useless in my case
Can you do bedliner after? Yes, but if your local shops are charging you less than $600. For me I planned to put in the Decked drawer so it doesn't matter whether I spray it or not. Even if the drawer scratch the bed I can always spray it later... you gotta sand the bed before spraying anyways.
Tonneau cover you can add later. Plenty of other options.
receiver hitch is something I'd just have the factory do... so your tow rating sticker is correct.
HK audio. Sure there are plenty other options but for people like me who don't really mess with audio the HK is plenty good. Is it the best of the best? probably not, but audio upgrade is one can of worms that I don't want to open at all so I went with it.
Floor mat can go aftermarket. Mine came with the truck for free so...
Trailer brake: this is one thing that you can add yourself but if you use the OE system you will need to code it in. If you go aftermarket... why go aftermarket if OE has that option to integrate it to your interior?
Now, here are the things that I think is better to get done by factory:
Body work stuff - color and sunroof
Driveline - rear gear ratio, 4x4, and locker (you can change it after but it's a lot of work and it costs way less to have the factory done instead)
Fuel tank - lots of work to swap gas tank (well, I hate swapping gas tank. done a few on customers' vehicles and absolutely hated it so maybe i'm biased) and you need to code it in
For me the one thing that I don't care about is offroad group and wheels and tires. You can always get aftermarket ones. In my case, suspension came off the truck with only under 400 miles on the clock and the skid plate came off a year ~12k miles on the clock. Wheels and tires came off at around 5k miles or so. These are the stuff that you can get way better aftermarket so no need to spend money on those.
Hope that helps.