Since OGR/GDAL treats the fid column as a special column; it is not included in the feature attributes when outputting a feature with OGR/GDAL.
So the selection of the fid column impacts the schema of the featuretype, therefore it should be included in the schema definition. Proposal to add a fid_column field to the tables[] element in the table definitions file like this:
geopackage_validator_version: 0.7.0
projection: 3035
tables:
- name: protected_site_nlps_nnn
geometry_column: geom
fid_column: fid