We ran into a situation where we had domain XPT files that were present in the package, but there wasn’t any corresponding information in the define.xml file for those domains. The validator does currently provide a means to detect this scenario (which really is an error in the define file creation), but it would be very useful if it did.
Please add an error or detection for cases where there is an XPT file included but no metadata for it in the define.xml file. In other words, if you have a define.xml file, then it should have metadata for all domain files provided.