The epsg code lookup seems to happen when encoding the bounds, native and latlon of the resource. And I guess for the native bounds this is wrong behavior since as you illustrated, much of the time this will be null. And for the lat lon bounding box the information is somewhat redundant.
So amending the envelope converter should remove any extensive lookups from the feature type encoding pipeline. I still think their will be a bit of info missing from a client trying to access OGC services pov, for instance in cases where a feature type is being reprojected on the fly, but I will worry about that when said case comes up.