Hi,
FYI, because JTS does not understand yet the OGC style four digit codes for XYZ geometries they are also not usable as source geometries from GeoPackage. The errors look like
Caused by: com.vividsolutions.jts.io.ParseException: Unknown WKB type 235
The issue gets probably fixed when this JTS pull request is merged and next JTS version is released
https://github.com/locationtech/jts/pull/92
Before that we should perhaps mention that limitation in the documentation that needs also some updates in any case because gpkg is now in core http://docs.geoserver.org/latest/en/user/community/geopkg/index.html
-Jukka Rahkonen-