Some of the reasons behind the suggestions (which are clearer when you view the associated pictures in the pdf):
"The Western reader’s eye tends to move from the upper-left corner of the dialog box to the lower right. Put the initial impression that you want to convey in the upper-left area (like the alert icon), and place the buttons that a user clicks in the lower right. Following this guideline makes it easier for users to identify what’s important in a dialog box."
"The button names in the save changes alert box correlate to the action users perform by pressing the button. The buttons read Save, Don’t Save, and Cancel. Using these verbs reinforces the identity of each possible action to the user. In other words, the Don’t Save label provides much more context for the user than the word No does."
"In order to prevent accidental clicks of the wrong button, you should always keep safe buttons apart from buttons that could cause data loss. Standardizing the location of buttons in a safe configuration provides an additional safeguard for the user. Place the Save button in the lower-right corner with the Cancel button to its left. Place the Don’t Save button left-aligned with the message text. Make the Save button the default button, which means that it should be linked to the Return or Enter key. This way, the user is less likely to accidentally click the Don’t Save button or activate it with a keystroke and cause irretrievable loss of data."
"Whenever possible, name a button with a verb that describes the action that it performs. Button names should be limited to one word whenever possible. You should never use more than three words for a button name."
One good justification for the Cancel->OK order is that it means the default button (usually the OK button, but also Save, Print etc) is always in the same position in the dialog -- far bottom right -- regardless of how many other buttons there are, and how wide they are. This gives consistency / familiarity / muscle memory.
It also lets you place "data loss" buttons well away, in the far bottom left, as "an additional safeguard for the user". On classic Mac OS, you always knew pressing a button towards the lower left corner, and set away from the other buttons, could spell trouble.
The problem with the Windows way of doing things is that the default button moves depending on the width and number of other buttons, and there is no "safe button place" and "unsafe button place".