First of all, the KB article you cited is rather old. It's dated July 13, 2004. There have been 2 major Windows OS releases since then and one more has entered a public beta.
Secondly, it sounds like you have misunderstood the note in the KB article.
The use of a right-justified Help menu in an application is not the recommended style for creating Windows applications. This article provides this information without recommending its use.
It means that although such a UI design (right-aligned Help menu) isn't recommended, this is the tutorial on how to create it.
As for the current guidelines on designing entry points to Help system in Windows applications, the current "Windows User Experience Interaction Guidelines" are quite clear:
- Use a Help button with the Help icon for the hub pages of control panel items. Place it in the upper-right corner. These buttons don't have a label, but have a tooltip that reads Help.
- F1 Help is optional. Users have grown accustomed to finding Help information related to the immediate context of the UI on the screen by pressing the F1 key, which is labeled Help on standard keyboards. You can include F1 Help if, for example, usability studies show that your users expect to find it, or your program UI is complex enough to benefit from contextual assistance.
- Programs with menu bars can have a Help menu category. For Help menu guidelines, see Menus.
These mean that the only Help button (not menu) can be placed in the upper-right corner, as we can observe in nearly any modern Microsoft application. Moreover, the Menu Guidelines don't have anything specific for Help menu except for the permission to have dedicated help items in multiple menu categories.
Now, a little bit of a historic overview.
I was able to find screenshots of old versions of Microsoft Word. In them, we can see that Microsoft indeed used to align Help menu to the right. However, the last time that happened was in 1991. I wish UI guidelines from those days were available to find out the thinking behind them, so instead simply enjoy the pictures. =)
Word for Windows 1.0 (1989)
Word for Dos 5.5 (1991)
Microsoft Word 6.0 (1994)
Microsoft Word 2007
However, this atavism has survived to the "modern times" in some software. For example, Norton Commander for Windows 2 had the right-aligned help menu despite being released in 1999:
and Total Commander still has it even today: