Having flats as an option makes sense if you're ordering factory direct - which will soon be possible with Fender - but it doesn't make sense from a retail standpoint, as stores don't want to be re-stringing instruments to customer's wishes, and Fender needs to put some strings on in order to properly set up the instrument before it goes out.
I was thinking of more mechanical "changes" that a lot of people would want stock, rather than have to get out a screwdriver to change, as the majority of people aren't "tweakers" like some of us. Even something as simple as a new string tree may be a big deal, and if a new 3-string tree/guide is put forward of the A string tuner, would leave a useless little hole in the middle of the headstock.
I guess covers would have been a good option and should be from the factory. I was thinking matching painted headstocks as well, but the poll only allows 10 choices.
I agree with the adjustable string spacing on the bridge - roller bridge probably.
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