gpkg with epsg:3812 data

**Is your feature request related to a problem? Please describe.**

at foss4g timisuara pygeoapi workshop we tried to add gpkg data in epsg:3812 format.
we had to set the parameter storage_crs to get the data projected to the correct projection (both in sqlitegpkg as well as ogr provider)
some questions:
- why does pygeoapi not deduce the storage_crs from the data
- setting the crs in the extent section seems to have no effect at all
- has this aspect been documented enough? we missed the aspect

Start by reproducing the EPSG:3812 GeoPackage case with the sqlitegpkg and ogr providers, comparing behavior with and without storage_crs and with a CRS in the extent section. Trace how each provider handles the storage CRS, then determine whether CRS deduction or clearer documentation is needed; done means the behavior is consistent or explicitly documented.

Written by the indexing model from the issue text.