[BUG] Geopackage with non-geographic input, outputs geometries with inverted X/Y axis

[bdon]

Describe the bug
The GeoPackageReader projects non-geographic sources incorrectly.

To Reproduce

• Convert a non-geographic source such as water polygons in web mercator https://osmdata.openstreetmap.de/data/water-polygons.html EPSG:3857 to GeoPackage: ogr2ogr -f GPKG water.gpkg input.shp
• Tile this as input using a profile, e.g.

  @Override
  public void processFeature(SourceFeature sourceFeature, FeatureCollector features) {
    features.polygon("water").setZoomRange(0,8);
  }

    Planetiler.create(args)
      .setProfile(new Water())
      .addGeoPackageSource("landcover", Path.of("data", "sources", "water.gpkg"), "https://example.com")
      .overwriteOutput(Path.of("data", "water.pmtiles"))
      .run();

Expected behavior
The output geometries are not tiled correctly, the X and Y axis are inverted.

Environment (please complete the following information):

• Hardware: M1 MacBook Pro
• OS: MacOS 15.2
• Java OpenJDK Runtime Environment Temurin-22.0.2+9
• Maven version: 3.9.9

Looks like the CRS initialization needs to look like CRS.decode("EPSG:4326", true); as is done in ShapefileReader.