Hi, Thanks for the return and for this proposal.
Could add here a link to your website based on StrapDown ? It could be helpful to see how others are using it.
You might be interested by other another project far more advanced : Jekyll (and Octopress !).
Anyway, to answer your question, no I haven't tried this. I'm pretty sure it could works quite well.
Do you know that it is possible to use some basic HTML markup in the markdown code ? An example is this example 2 where you can use a <script> tag in the main markdown page.
A second example is a page with MathJax enabled : example 3.
But it might also not work, as StrapDown basically rewrites the entire page (it adds bootstrap style sheets to the head, and change the entire body).
You are welcome to try, and give feedback there. (just to precise : I'm not really interested by modifying any part of the StrapDown code, so don't feel obligated to post a pushing request if you change it)