All of this would seem to cancel out any of the cost advantage of purchasing a Giant in the first place. I see it as Giant building-in incompatibility to dissuade people from buying their bikes to donate parts to another frame. All this guff about increased stiffness - the increase would be marginal to non-existent.
You also have to factor in the unsellable fork and stem you are left over with after this conversion.
They're just protecting their brand.
Before today, this was pretty much my view as well. Having read Pinkbikes article and done a little searching though, it would seem that the bigger fork steerers can be used on bikes with a 44mm ID headtube. Giant hasnt changed the frame from 2 years ago when nobody complained, all they've done is put a new headset in to fit a fork with a bigger steerer - the headset isnt proprietry, nor is the steerer size.
Sure, if you want to change the fork to another bike, you'll need a new headset, and make sure the ID is the same. but putting an aftermarket fork seems pretty easy. The only real problem is for people who cant have Giant stems on their bikes, coz they can only have syntace at this stage