the dealer wouldn't give me the number. I am concerned because evidentially the dealer wants the difference between the warranty repair amount and the actual out of pocket amount.
Can you tell what about them is making noise? The warranty may not cover the strut cylinder itself if considered a wear item, but I am not so sure about the spring, spring seat, upper mount bearing, and bumper, some of which can be argued are suspension parts separate from the strut, that if you buy a new strut it does not come with these parts, and they don't need replaced if only the strut is worn out.
I would ask more questions of the dealer, is this going to be covered under a TSB (which doesn't necessarily mean anyone else is obligated to pay anything), or warranty? If TSB, with no warranty coverage, Ford could opt to pay nothing which is usually the case, or pay any % of it and you are left paying the difference.
If it is instead warranty covered, then you should not have to pay anything (except possibly a deductible?) , including not a difference between what Ford pays shops for warranty work, versus what they would have charged you if not under warranty. It is normal that a shop makes less money on warranty work and just accepts it as part of being a Ford dealer shop.
Both (how many, which ones?) struts are making noise? It seems a little strange that they'd both go out so soon unless the strut manufacturer had a bad run, or unless you were driving it like you stole it.

Then again there are lots of hills and curves here, it's not abnormal for me to go through a pair of struts or shocks in 50K mi., where that amount of wear would be more acceptable to me at 50K if I were just freeway cruising, especially in a lower center of gravity vehicle, but they aren't making noise, just failing to dampen suspension travel enough.