Yes, the stock boxes have different comments than those generated by the system (if you "create a new custom island" it'll generate code as I specified); the end coding is still the same, with this still being where HTML coding (the body of your Custom Island) goes
Comments in the stock islands in the stock package will be updated in a future release to reflect the comments from when the system generates a new Custom Island, but this will only affect new installs (as a basic upgrade step is to not upload the cache_builders/custom folder).