OK I see you point. I'll add in something to handle this in the sysex handling.
Since the MIS that is purely a way to describe how to talk to a device, the assumption is that if the chart->GM settings are set to XG/GS etc that the application should follow all the XG/GS specifications. That being said I'm hoping that either I or someone else would be able to have a public spec that describes this.
The idea being that say something like a Yamaha CS1X* which has the XG spec + it's own extra set of params/sysex. The MIS file would say it has XG, so go reference the XG file and the document would only list the extra information required for the CS1X.
* note this is purely off memory and I may be wrong