In this particular case it sounds like your resolver was set up to try an external resolution first and then append an internal domain if the external resolution failed. And as you say, this clearly worked just fine for a long, long time. Then it suddenly started failing one day, for reasons unrelated to anything you changed.
At this point, most people would find it reasonable to blame the external change for breaking their fully functional, correctly working, "properly configured" setup. Some, perhaps contrarian or perhaps more cautious, would note that the "properly configured" approach only worked so long as external systems played ball. I think it might be the case that you were bitten by this assumption that seemed safe at the time, leading to the awkward and uncomfortable conclusion that your systems were indeed misconfigured.
I would argue that, of the two options, option B is the less onerous one, and less restrictive on the future growth of the Internet. It's not that hard to set up some aliases to be able to SSH quickly into the right hosts without having to manually type out longer paths.
I mean, I THINK this is "properly configured", but it also isn't a huge deal to avoid. Just was annoying when it started happening. Didn't FEEL like I was misconfigured. :-)