This has been solved with DEVONthink 3.8.
Release notes:
Added hidden preference
RawMarkdownPasting
to avoid the conversion or formatting of links or rich text content when pasting into a Markdown file. This option is off by default.
From help Documentation > Appendix > Hidden preferences
:
RawMarkdownPasting: When pasting rich content into a Markdown file, the formatting is converted to Markdown. Enable this to ignore formatting and paste as raw plain text.
Click the link in the help to enable the hidden preference.
Thanks for listening to users!