The approach I'd really like to use is to persist log configuration between boots (via serialization or something). This way the boot logger config is only used the first time you boot. Then subsequent boots would just apply the delta of the old config to the new config (which would normally be 0) during a regular boot. This way the server boots up with a regular log configuration.
Granted this would be a bit of a pain to implement since the LogManager currently does not have the notion of a persistent configuration, and the diff logic won't be trivial. That's why I have put it off.