And you actually use all of those headphone jacks?
I bought one of those original iPhones, paid full price for it too (and all I got was this stupid gift card ;-). And I used the headphones they supplied with them, and never had a problem. But that was also a very different kind of adapter to sell. Moving people over to lightning will be a little easier because they can promise better audio, and the included earbuds will showcase that. A 3.5mm adapter in the box will deter people from using the Lightning headphones and opting to invest more in the quality of their audio. Lightning can do HQ audio now, but it's so expensive that nobody's really looking past the cheap low-cost alternative they've been using. But what Apple really wants is for customers to move to wireless. But it's still too expensive. Apple needs to turn up demand to get developers to offer better quality products at lower prices. Putting an adapter in the box to continue using their old, cheap, often low quality 3.5mm products is not going to motivate customers to do that.
And no, Apple is not going to upset "hundreds of millions" of customers with the iPhone 7, considering there's only about 475 million active iPhones out in the world as it is. They'll upset a fraction of the 120 million or so iPhone 7s they sell. But not all of them. And I'd be very surprised Apple would make this move at this point without a pretty good idea of how their customer base was going to react. And there will be inexpensive adapters for sale, so nobody's old headphones are going to become unusable. I doubt Apple will charge more than $20 themselves, and cheap Chinese adapters can be had for probably less than $10.
So the fact Apple will likely give customers a free pair of Lightning headphones, will satisfy many of them who actually use those headphones primarily. The custom headphone users are going to grouse, but it's the total number of those customers that's going to make the difference. When the iPhone was new, only Apple's headphones would work with it, and that was a problem because there were not any other good options like Bluetooth, or Airplay. 10 years later and there's tons of reasonably good wireless options, and Apple's headphones have improved quite a bit as well.
As for what's in the iPhone box, I could imagine Apple coming up with a unique Lightning connector with a built-in 3.5mm plug so that their headphones will work with Apple's other non-Lightning equipped products (as it will take them a while to add Lightning ports to all of their current products). But I don't see them encouraging the use of 3.5mm products out of the box. Unlike the original iPhone which Apple miscalculated the desire of customers to use their own headphones, you can bet the sales clerks at the Apple Store will be asking the customer if they'd like to buy a 3.5mm adapter for use with their current headphones. I never knew that my old headphones wouldn't work with Apple's new iPhone when I bought it. And that's probably more upsetting than knowing and being able to do something about it when I was buying it, rather than after I got home, especially when I found out all it did was adapt the plug shape to another dimension. At least the Lightning adapter purports to offer a higher quality of sound.
