I wouldn't overthink it and wouldn't worry too much about resale (if anything, you often lose on the options not typical for your trim level)

do you plan to 5th/goose? if yes get 5th wheel prep/goose prep. If not, you can get it aftermarket
Do you plan to tow about everyday? if yes get TPMS. If not, you can get it aftermarket
Do you plan to haul a bunch of stuff? If yes, factory liner is fine IMO. If not, you can get aftermarket

Now, some of this stuff is not easily available on the aftermarket...
To me, LEDs are mostly aesthetics
Some people love the functionality of BLIS, Cameras, tow tech, etc. Some people don't use them at all. Might want to test drive if you aren't familiar. Having had BLIS and cameras in the past, I've come to rely on them.

 

I think it's more fair to say they each have their pros and cons.

I just personally like the B&W better because you can store the ball in the hitch when you don't want it up and I already owned a 4" offset ball extender. https://www.etrailer.com/Hitch-Ball/...WGNXA4085.html
I'm not sure if you can get one for the factory hitch or not.

With the B&W you have to add a 7-way plug and cut the bed for that and the hitch itself of course. You really won't know if the tech that installs the hitch touched up the paint on the exposed aluminum properly unless you stand there and watch.

I think the factory set up might be a little cheaper and it certainly looks nice. It's also covered in the warranty and the holes are cut at the factory.

You have to pick which works best for you.

 

This is my second factory bed liner. I had zero problems with the first one and I doubt I'll have problems with the bed liner on my F-350. I suspect that if you tried hard enough you could rip up a Line-X bed liner and make it look almost as bad.

 

Keep in mind this video is done by a Line-X dealer with the sole intention of trying to make the Line-X liner seem far superior. Line-X "scuffs" up your bed which removes paint. Ford just starts with a very clean painted bed, applies an adhesion promoter, and sprays in the liner. I've had three Ford trucks with the factory spray in liner and four with aftermarket liners. My truck beds are used like truck beds...I think nothing of putting a 2,000-lb pallet load of wood pellets skidded on by a fork truck, or using a tractor to lower a 2500lb implement into the bed. Or throw in wood I've cut down. I leave heavy chains, hitches, you name it in the bed. NONE of the factory liners have ever failed in any way...they don't peel, chip, or come off. I like the Ford oval embossed into the front of the bed. They look great. BUT...they are the most slippery bed liner I've had...great for skidding a heavy pallet, poor for having it stay in place. Fuel cans slide all over the bed. I don't like this. And, Ford does not spray under the Box Link cleats; you will see paint. Aftermarket spray in liners typically remove them, the standard bed tie downs, maybe the bed bolts...and then spray. My favorite after market liner is Line-X; that's what's in my current truck. But my first 2017 dually had a Ford liner.

 

One of the big things they point out in the video above isn't just the quality of the material itself. It's the number of places that the factory doesn't put the bed liner. Line-X will completely surround every part of the interior portion of the tailgate, including all the way to the end of the bed, where factory stops a bit short, and doesn't go past the end corner.

 

Ford F-350 - a 250 rides a little bit better and might be cheaper to register. But you give up some payload and by extension, towing. You know how much weight you need to carry and how much you need to tow. Purchase the right model for right now and the future. But I will say this generation of F-250 seems to be significantly "tougher" when it comes to rear springs. They don't squat as much.

11400 gvwr package - the difference is like 100lbs. I don't see this as a big deal. Only select it if it benefits you on registration. It's a paper package only.

Camper pkg - likely increases payload and with that reduces ride comfort. Also provides a paper certification for a slide-in bed camper, as well as a rear roll bar (which only comes as standard on a dually).

FX4 pkg - Rancho "branded" shocks are no longer offered (they weren't great anyway) plus the price increased for this package for 2018. Seems like you get Hill Descent Control, a skid plate on the gas tank and one under the transfer case, all-terrain tires, and a forced upgrade to a locking rear differential...plus the stickers on the bed. Keep in mind the following: by purchasing a $15 factory dash switch and by using FORScan, you can add Hill Descent Control to any truck...for the cost of the switch. The skid plate under the fuel tank is reasonably substantial; the one under the transfer case seems small and useless. There is no skid plate under the engine / transmission. The All Terrain tires are likely going to be GoodYear Wrangler Adventure w/ Kevlar. So far, I'm reasonably pleased by these tires. They seem to do all things well, but not great (snow / mud / rain / quietness / tread wear / fuel economy). I'm content with them...better than the Michelins except for fuel economy and quietness.

Tow Technology pkg - I tow for a living and for pleasure, and I did not get this package on my 2017 Lariat Ultimate dually or my 2017 XLT Premium. I think it is a nice package and makes life easier so I'd recommend it, but also be aware you can tow very well without it.

5th wheel/Gooseneck prep pkg - Definitely recommend. Let Ford cut the holes in your bed precisely and add the 7-pin trailer plug in your bed. Yes, it can be done aftermarket, but Ford's cost is fair and it will be done right.

Spray in Bed liner - the factory liner is now getting more expensive. It looks nice and holds up just fine; its also nice having this "already done" when you get your new truck instead of having to leave it at a shop for a day. Nevertheless, it is one of the most slippery liners I've used, and I can get a superior Line-X liner for less money.

Blis - The Super Duty mirrors don't have any blind spots, so this feature really isn't needed...BUT...the rear cross-traffic can be a very nice feature, especially on a long Super Duty pickup. And sometimes its nice to have the little orange reminder in the mirror even though you can see the car next to you if you just bother to look. I'd recommend it.

Hitch kit Gooseneck - the Ford / Reese hitch is quality, but aftermarket options may be both higher quality and a better deal.

Individual TPMS /Trailer Prep kit - Nice feature, might help you prevent a blowout or save a little fuel or tire wear. But I doubt it really makes much of a difference in real life.

Quad-Beam LED Headlamps - These are very nice. Had them on my 2017 dually, and have the standard halogens on my 2017 XLT. They are very bright, definitely an upgrade over standard. They look terrific, and realistically cannot be touched for the price of this option. Aftermarket versions might be cheaper, and might even be brighter, but will never look as good, and might even be illegal. On the other hand, the standard "quad beam" halogen lights have a unique look and are a nice upgrade over the previous generation headlights. They are reasonably good.

Wheel well liners - Given that the bed is now aluminum and won't rust, I don't see the use for these, unless for aesthetics.