Point 1 states Adobe Flash has proprietary features and the standardized open feature sets of HTML5, CSS, and JS should be used instead.
Point 5 states 3rd party layers limits development to the standardized features and leaves out the proprietary features that makes Apple unique.
Point 1 is in reference to the lack of Flash within Safari.
Point 5 is in reference to banning applications originally written in Flash.
Point 1 is in reference to a non-Apple product
Point 5 is in reference to an Apple product
With point 1, if developers are going to make a website, and they ditch flash, their work would work everywhere well (iPhone/iPad/iPod, Android, WebOS, Symbian, and Blackberry OS 6, as well as on the desktop). They wouldn't be limited to the platforms Adobe decides to support (or decides to support well).
With point 2, if you're going to make a native app for the iPhone, make one for the iPhone. Don't make one with Flash, which may not get around to supporting things like GameCenter, or multitasking, or any of the other hundreds of things Apple adds in new releases.
Choosing Flash for either one makes a substandard experience compared to the other options available.
While web applications and native applications are different domains, they are not different enough to mean different reasoning can be used. An end user doesn't really care if something is built using HTML5, flash, or compiled natively. They just care that it looks cool and does cool things.
This is the classic fallacy of exhaustive hypotheses of the 2nd order, a.k.a. "a false dichotomy" or "the fallacy of the excluded middle".
There is a third possibilty: that both are good, and that which is better depends upon the nature of the app one wants to create. This third missing case also happens to be the reality of the situation — there are tradeoffs, and one selects which is better according to the upsides that one desires versus the downsides one is willing to abide.
(Surely you're not claiming that there are no tradeoffs between the native API and web technologies! I can think of several, not the least of which is the limited rate at which innovation can be brought to the web API.)
Remember, this is not an essay about why everyone else should support Apple's actions. It is an essay about why Apple thinks its actions are good for it.
Hidden in that of course is the lack of concern for what's good for the consumer.
I don't even think Jobs tried to hide this very well. It's pretty clear he is arguing from the perspective of what is best for Apple, and clearly and coherently explaining why.
Point 5 states that ubiquitous Flash co-opts the rate of advancement of the mobile platforms it runs on. E.g. you can't effectively differentiate your device by adding a new sensor, API or capability, because Flash won't bother to support it until the hardware is standard.
It's the same basic argument: Flash becomes the platform, it's not a particularly good one and it's not a particularly good situation for developers.
Would you rather Apple compete with Google, RIM, Microsoft and HP/Palm for developers, or have them compete with interchangeable Flash-playing-boxes, leaving developers to Adobe's whims?