Commit fbbe0cfe29020313ae44fb2a6afa87c2951ae028 indicates that the rationale for having this disabled is to tolerate manual additions/removals of binpkgs in the PKGDIR. I don't think there are many people doing this, so it should be safe to enable this by default for quicker operations with PKGDIR.
While I actually do this at times, I've always run `emaint --fix binhost` to update the index after while assuming it was needed (never really noticed this feature, and now would rather it be enabled, or at least for the machine using sshfs for this). I'm under the impression most people update it as needed too, but who knows.
I've been doing the same as Ionen and feel the same too.