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My two cents to just those two points you raised:

• users may mistakenly take in code comments as part of the provided solution

  The syntax highlighting prevents that very well, for example:

    #!/bin/bash
    a=~/dir # fill variable a
  

  Unfortunately syntax highlighting doesn’t seem to work here on meta, but on main the comment would appear greyed out if the code block was preceded by <!-- language: lang-bash -->.

• its not easy to point to a specific code section without repeating it in the text

  You can use the usual formatting inside code blocks if you use the html markup, e.g.

    <pre><code>#!/bin/<i>bash</i> # italics
    a=<b>~/dir</b> # bold</code></pre>
  

  gives:

  #!/bin/bash # italics
    a=~/dir # bold

  • AU Markdown help – Inline HTML
  • What HTML tags are allowed on Stack Exchange sites?