I doubt this is the most efficent workaround, but it solved my issue.
writetable(table, filename, 'WriteVariableNames', 0,...
    'FileType', 'text', 'Delimiter', 'space', 'QuoteStrings', false)
content = fileread(filename);
 % Update the file
 content = {cell2mat(header{:}); content};
 % go back and remove empty lines
newcontent = regexprep(content, {'\r', '\n\n+'}, {'', '\n'});
 % write the full file
 writecell(newcontent, filename, 'FileType', 'text', 'QuoteStrings', false);


