Zip files produced by rules_pkg do not contain directory entries. For example, they look like this:

META-INF/MANIFEST.MF
xds/one.xsd
xds/two.xst

Although technically not required by the spec, a convention is to add directory entries to zip files (0 bytes, file name ending with /). A lot of tools seem to follow/implement this convention.

Expected:

META-INF/
META-INF/MANIFEST.MF
xds/
xds/one.xsd
xds/two.xst

Missing directory entries may cause issues with the Java ecosystem, which seems to heavily rely on the directory entries. For example, see this Spring Framework issue:
spring-projects/spring-framework#28230 (comment)