Simple fact is that HTML support is different in them because mail clients are so old, or others are allowed to operate in browsers where not all CSS or even HTML can be applied in a secure manner.
Older clients have outdated browsers that you'll likely NEVER see brought up to standards; what with Opera's standalone aging like milk, and thunderbird lagging behind the firefox on which it's even built. Don't even get me STARTED on older clients like Eudora or Outlook.
But more so, external style cannot be applied to a subsection of a web page unless they force it into an iframe, which has all sorts of issues of it's own which is why external CSS is usually ignored. Inline CSS is often stripped by the tag strippers who don't want you turning things on or off... and media queries shouldn't even play into it since the layout should be controlled by the page it's being shown inside (for webmail) or the client itself, NOT your mail.
Simply put you shouldn't rely on HTML or CSS in an e-mail if you give a flying purple fish about people actually using them. Whilst I realize the artsy fartsy types get a raging chodo over their goofy PSD based layout asshattery, that garbage has ZERO damned business in an e-mail which is why a great many places use HTML only e-mail as a trigger for spam detection! (if you send multipart as both text/html and text/plain, you're fine)
Bottom line, you want to use that rubbish HTML e-mail garbage, use HTML 3.2 and two or three of the small things found in the proprietary garbage that wormed it's way into 4 tranny. Do NOT rely on CSS, do NOT rely on anything from 4 strict or 5. That's what's supported, and is all that is EVER likely to be supported... and even then be DAMNED sure you send multipart with a plaintext copy or a great many mail servers will flat out reject it on the assumption that no legitimate e-mail has any damned business even having HTML in it in the first place!
You want HTML, build a honking website and provide the URI in the mail. Anything else is scam artist BS just begging to get your mail kicked to the junk box... no matter how many marketing and "design" re-re's cream their panties over the idea of their bloated arsty junk being shoved in people's faces!