The indiewebify.me site has a parser that is looking at the two sites to see that they not only point at each other, but it requires that the two links have the rel=”me” microformat on them. Most don’t, but this doesn’t mean too much in practice. Whether or not they both have rel=”me”, the only way both sites could point at each other indicates that you “own” or control them both. Kevin marks has proposed/built an interesting decentralized verification service based on them. His version is certainly much better distributed than Twitter’s broken verification set up.
Other than having a stronger two-way ownership indicator, what do you get out of them? As you mention, some have the ability to be used with IndieAuth. Those that can be used with IndieAuth are relying on the service (like Twitter or Github) having a OAuth implementation for signing into their services. This allows an indie site to piggyback on another services’ OAuth implementation without having to go through the trouble to build one themselves, which can be a lot of work to do, much less do correctly (securely). Most of the services you see not linking back not only don’t add the rel=”me” tag, but they also don’t support OAuth, so you wouldn’t get too much more out of having the correct reciprocal link anyway.
Incidentally, one of the benefits the rel=”me” links do have is that they allow you to use your website to log into the IndieWeb wiki to participate directly in that part of the community. (Give it a try!)
Some services like Brid.gy get around services like Instagram or Facebook not having a physical rel=”me” microformat because they’re relying on looking at the appropriate data (usually via API) on your profile page to see if it links back (either in your website field or typically in your bio).
Don’t be overly concerned that the vast majority of sites appear not to link back even if you’ve got links on both pointing back. (And if you think your batting average is bad with only 4 of 43, just imagine how many of my 200+ sites do?!)
Some of these building blocks will likely add a lot more value later on as more and more sites explicitly indicate their relationship to and from each other.