I don't doubt that those are the actual reasons, but that's not really the point. All it means is that they're pushing off their (engineering) problems on their users. Apple has a long history of deprecating stuff that (at the time) people thought was premature - but in essentially all the other cases it turns out that the new thing really is better. Serial ports, the floppy drive, non-USB connectors, CD drives in laptops, even replaceable batteries - there are tangible benefits to switching to the new thing, and they usually relate to speed, capacity, or physical size.
The headphone jack is slightly thicker than a Lightning connector (the only remaining jack) - but they didn't make the phone thinner to take advantage of the extra depth. And other than the connector itself a Lightning headphone is worse in every way, because headphones are driven by your ear technology, not the phone's. The newest fanciest Lightning headphones in 5 years (assuming this decision sticks) will never be more than today's headphones plus a built-in Lightning dongle.
What does this decision get me as a user? Let's go through. Headphones are headphones; there's two channels of audio that are the result of a varying electrical signal. I don't really care what the cord to the device looks like and considerations like "do these phones work with other things? do other phones work with this?" easily dominate that area. I guess this lets them use a little extra power but there was already more than enough output to damage your ears. If there were wild battery life improvements... maybe? But someone on the other thread did the math and a headphone jack's volume of battery is good for ~12 minutes. Meh. What about water resistance? Other phones have no problems with the IP67 rating and a headphone jack - I have no doubt that it was easier for Apple's engineers, but Apple used to not push their problems on their users.
So what does that leave? They wouldn't be able to have a force-sensitive home button? Honestly I'd rather have the headphone jack. Or just get rid of the home button - it works just fine for Android - or at least make it oblate or rectangular rather than round.
I have had every non-S model iPhone since the 3G, so I'm "due" to buy this one. In addition I have apps that I rely on that only work on iOS. It should be a slam dunk. But... honestly? I knew someday I'd lose the reason to buy an iPhone, and this might be that day. Not just the headphone jack, but the whole package. It doesn't look like a bad phone as such, but the only thing I'm really interested in is the waterproofing. And I'm not careless enough with my phone that getting it ruined is a big risk. The headphone jack thing isn't a dealbreaker, mostly because I don't listen to music much on my phone, but it's damn close.
Honestly Apple is just out of ideas. I bought a new MBP last year and it was the first hardware purchase I made in my entire life that I wasn't excited about. Roughly as functional as the 5-year-old one it replaced, more in some ways and less in others, but the same price. I needed a new one because the older one wasn't really working but boy did they manage to turn something I used to enjoy into something kind of boring and depressing. I'm still annoyed about the large size of the smallest iPhone still available - I was in London a few months ago and had to use my (out of contract and unlocked) iPhone 5, and it was sooooo nice. I assumed I'd gotten used to the wider width, but nope - and I didn't miss the extra screen at all.