The _isSelf command can be issued while digesting a replica set config if we cannot determine the "is self" answer by other means. Those other means seem to be unable to determine the "is self" on some platforms [*], so we fall back to issuing an _isSelf on the network.
In the referenced BFs, this was happening in a restarted single-node replica set. When it restarts, it issues _isSelf and fails because it has no key file (single-node replica sets don't think they need a key file) and so won't accept __system user commands.
The fix is to just override _isSelf's Command to make requiresAuth() return false.
[*] Debian builders and on my Ubuntu 18.04 workstation, but not other evergreen builders like RHEL.