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);