As can be seen from the snippet below:
String userDefinedCrsIdentifier = (String)envelope.get( "srsName" );
String nativeCrsWkt = (String)envelope.get("crs");
CoordinateReferenceSystem crs = CRS.parseWKT(nativeCrsWkt);
coverage.setNativeCRS( crs );
ReferencedEnvelope bounds = new ReferencedEnvelope(
(Double) envelope.get( "x1" ), (Double) envelope.get( "x2" ),
(Double) envelope.get( "y1" ), (Double) envelope.get( "y2" ),
The catalog importer reads the bounds projected in the user defined CRS and associates to them the native CRS, so resulting on a final Coverage Envelope which has wrong coordinates against its CRS.
Of course this error can cuse unexpected GeoServer behavior when threating Rasters.