This problem could be overcome by allowing multiple abbreviation declarations in a document using the existing Markdown Extra syntax. Just use the first abbreviation declaration below the use of that abbreviation. For example:
CSS
Another use of CSS
*[CSS]: Cross Site Scripting
CSS
*[CSS]: Cascading Style Sheets
Yet another use of CSS.
would produce:
<p><abbr title="Cross Site Scripting">CSS</abbr></p>
<p>Another use of <abbr title="Cross Site Scripting">CSS</abbr></p>
<p><abbr title="Cascading Style Sheets">CSS</abbr></p>
<p>Yet another use of <abbr title="Cascading Style Sheets">CSS</abbr></p>
The actual placement of the abbreviation definition wouldn’t matter so long as it was after the use of definition. If no further definition is listed, the last defined definition will be used, as in the “Yet another use of CSS.” example. I can imagine definitions being listed at the end of a chapter or section to keep the document tidy though.