the correct fix is to change extension to the files, or to explain no-intro guys that their creating unsupportable sets by removing the header with no advice to the users.
It should be noted that No-Intro supplies a template to use with clrmame pro to ignore the headers when checking the checksum. However, people still remove the headers in order to fill their romsets. This also applies to other systems where the header is ignored but needed
This is why No-Intro specifies the lnx extension. It is purely the users at fault.