We've figured out that having:
"convertWikiMarkup": true,in the settings.json configuration of the tm4j-file-converter prevents text between brackets to be removed.
The point 2 with parentheses was not an issue after all (that text was also in some brackets)
So the remaining issue here is the lost formatting of bullets / text decoration such as bold, italics and headings in test steps: these are lost after export of Zephyr test cases to XML.
Bullets remain in the XML but are not interpreted as separate lines in Import from file, probably due to line breaks are gone as well during the export to XML.
I'm posting a question in Zephyr forum in regards to XML export