I guess what I am really asking is ..... Does any Perl XML modules behave in the same way? If the answer to this is yes, then I could have problems in the future.
this sounds more relevant to Perl Monks... No, the Perl XML modules will behave correctly. Sometimes emacs modes use rather simple methods to do syntax colouring, for ease of programming and speed. The XML:: suite of modules, however, is designed to behave correctly ;-). That is, if your input is valid XML, it should parse fine -- everything else would be a bug.