In picture #2 you can sort of see the rhizome peeking out, so while it may be a good idea to bring it up bit, I doubt it would be detrimental to the plant if it was kept in the current position. I have kept Java ferns healthy even with completely buried rhizomes - not that I really advise doing that, but I don't think that the rhizome-above-the-substrate is really as huge of a deal as some make it out to be. Since they can be so hard to plant when anchoring just the roots, some people will bury the rhizome for just a couple weeks, so the roots can take hold of the substrate, and then raise it back up. I have done that as well on some Java ferns that just don't want to be planted.
