A few weeks ago, GeoPackage achieved a new milestone when OGC adopted "OGC GeoPackage Extension for Tiled Gridded Coverage Data" (http://docs.opengeospatial.org/is/17-066r1/17-066r1.html). This is the first time OGC has adopted a GeoPackage extension outside of the encoding standard itself. We did this because we wanted the flexibility to create and revise the standard at our own pace without being constrained with the release schedule of the core standard (or vice versa).
What does this mean with regards to OGC compliance? By definition, a GeoPackage may contain extensions along with tiles, features, and attributes. An OGC-compliant GeoPackage is one that contains OGC-adopted extensions. The encoding standard itself currently has seven extensions (three of the original ten were later deprecated) and this new one is the eighth. They all have equal footing and the upcoming minor revision of the GeoPackage Executable Test Suite will include tests for all of them.
If OGC compliance isn't important to you, that's fine too. The extension mechanism is your friend. Use the gpkg_extensions table to advertise what extensions you are using (OGC-adopted or otherwise) and let client applications inspect the table and adjust their capabilities accordingly. You are always free to include non-adopted extensions in your GeoPackages too (no one is going to stop you) but OGC is unable to verify foreign extensions so there is no guarantee that they are fit for any particular purpose or that they will not cause compatibility issues with other software.