Ok, now I see what you're referring to. There are actually three unique fact sheets:
One covers the 534 & 536 (automotive).
One covers the 535 (applications processor).
One covers the 537 (also referred to as an applications processor).
The sheets for the 534/536 and the 537 state IEEE-1588 HW support for ethernet, but the sheet for the 535 simply says 10/100 Ethernet. As you say, the block diagrams imply that ALL have the 1588 HW support! Ok, I feel totally justified for being confused about this now! :-)
Regarding IEEE1588 apps in general, I'd be interested in anything you dig up. I am on the steep slope of the learning curve here for iMX53 and IEEE-1588. I'm having a hard time digesting the notion that an application in Linux can use this, so I'd love to see some kind of Linux based example that successfully takes advantage of it.