Let's see if I can help answer some of your questions ...
Yes you can probably add on after the fact, but it's almost always significantly cheaper and easier to get whatever features you want/need from the factory than try to get those added on after the fact. Finding all the necessary parts and getting the vehicle re-programmed isn't always easy or straight forward. The dealer may not even be able to or want to do the work either. For any upgrades/changes you want to do after the fact, you may want to look through the forums here to see if anyone has done it before which will make your life a lot easier if you plan on doing the work yourself. I kick myself for overlooking the missing cab lights on the truck. They are a $50 option, but will cost me around $150 in parts plus any labor to install; though I suppose I could just poke the holes in my roof myself.
The prices that dealers quote you tend to be based upon whatever factory and dealer incentives are going on that month, which doesn't always tell the whole picture. You'd be best off understanding what those incentives are and how you actually qualify for those before taking the dealer at their word. In regards to other costs and fees, you can expect to also pay tax, title, documentation, and possibly destination fees if they haven't already rolled those up into the vehicle price. You'll also want to calculate for any dealer add-ons you might be wanting to do such as Ziebart coating, bed liners, under seat storage, or whatever you might want to purchase extra. Once you get past the first salesman who sells you the car, be aware of the second salesman, whom many forget about, which is the F&I manager. The F&I manager may run your credit, setup the loan, and do all the paperwork at the end, but their most important job is to sell you more stuff after you've already worked out your deal with the first salesman. They are going to try to sell you on any add-ons, warranty, and vehicle protection stuff. So do plan for the second salesman and the extra stuff they will probably convince you to buy. Not saying that stuff is bad, but many forget about that part when negotiating with the first salesman and end up paying more than they planned/budgeted for.