Wrt 1: Checking around I would say it is an issue with the markdown generator. The stars/asterisks are markdown syntax for emphasis. They are also limited to inline use, i.e. cannot cross lines, while the .man [emph] command is ok with application on multi-line text. The generator is not taking this into account and simply emits the md syntax without breaking lines apart and marking each separately.

Wrt 2: The trailing bracket is actually present. It just somehow moved to the next line, after the example. Checking ... In the .man it is definitely part of the example.  And in the generated .md it is separated from the example by a blank line. So the input is ok, and the fossil markdown rendering does the correct thing too. The issue is in the markdown generator. Again.

So, both problem are issues with the new markdown generator, and not with the manpage.