I believe this is only designed to be used in conjunction with Internet Explorer.

Yup. That's because MSIE is the browser that is affected by it the most. URL Obfuscation is what the term is and what we're seeing a rise on is "phishing" using that obfuscation. Making URLs "neat" and "clean" isn't always the best.

In addition, MS needs to have an option to remove HTML from incoming (not just outbound) emails and have it set as default rather than having HTML emails set as default.

Interesting in that link I found another article and it stated the following:

To turn on the Read all standard mail in plain text option, follow these steps:

1. Start Outlook 2003.
2. On the Tools menu, click Options.
3. On the Preferences tab, in the E-mail area, click E-mail Options.
4. In the Message handling area, click to select the Read all standard mail in plain text check box.

Note By default, the Read all standard mail in plain text option is turned off.
This is, of course, for Outlook 2003 ONLY. Although IIRC the default of HTML email is turn on for all Outlooks.