I felt that @cholland answer was good, but I didn't like the extra xml work. So here is a solution to strip the whitespace from a copy of the xml file which is the root cause of the unwanted elements.
fid = fopen('tmpCopy.xml','wt');
str = regexprep(fileread(filename),'[\n\r]+',' ');
str = regexprep(str,'>[\s]*<','><');
fprintf(fid,'%s', str);
fclose(fid);