My opinion may vary from yours.  I've ordered 3 out of 5 Ford trucks, and probably wouldn't do anything else in the future.  My experience is Ford only.  Remember you buy a truck every few years--the dealers do it every day.  So, you need to go armed with information.  The big dealers would rather sell a truck on the lot than order, but they'll order to make a sale.  Your most powerful bargaining technique is to not make a purchase if you don't get what you want--the dealers know that there is a 90% chance that they will not make a sale if you leave.  Don't be surprised if they tell you that 2017 ordering is cut off--this is about the time of year that it happens.  Then, they won't know prices and options until mid-summer.  Dealers absolutely can lock in the rebates available at order time and then give you additional rebates in effect at delivery.  It takes a little more work for them registering the order with Ford, and some will not do it.  My dealer did it for me and I got an additional $750 off.  Invoice is not dealer cost, it is just an accounting point, and can be used for a negotiating point.  The build your truck site can be strange at times.  For instance, a few years ago, it wouldn't let you select the heavy option on an F-150 unless first selected the correct rear axle ratio, which one typically does not know.  I complained and Ford fixed it so you could pick the package,  and then the site would pick the correct axle ratio.  Also, it can be a struggle with Ford to get the options you want in the combinations that you want, as others have said.
Keep asking questions on this thread, and we'll share our specific experiences.