I'll answer my own question with my view:
In view of the very few possibilitiesvery few possibilities that markdown offers to format answer and basically no customizability of the markup, one can barely speak of a markup language (there even is not syntax for emphasis, only commands for typesetting such as italics, bold, and bold italic). Moreover, logical markup is not used to parse answers by algorithms (other than rendering). Hence, my view is that markdown shall be used to format the posts to appear as needed.
Finally, other SE sites seem to use blockquotes for other purposes than quotes: A comment to StrongBad's question over at english.stackexchange states that
…the main use of block quotes here is to format and separate examples of word usage.
Over as tex.stackexchange I also noticed the pattern that people used blockquotes to emphasize paragraphs.