I think it is correct. Because logging should be bootstrapped very before the first caller tries to access it. Consider that some lib in $maven.home/lib/*.jar would like to log but the log config is not yet available. That would probably fail.
Regardless of this, I would stick to the same answer I have given on stack overflow almost four years ago:
You never provide a log implementation. The client application has to do so. Otherwhise this would be a violation of separation of concerns. Don't do any assumptions about an unknown client.
Logging and its configuration is solely the task of the client and not a dependency. Everything else is problem.
For example, if conf/logging is the first entry, the logging library could provide default configuration, which the user would still be able override through explicit configuration.
We have provisioned the conf/logging directory for that, didn't we? We never expect someone to put a logback.xml into ext.
If one of your ext JARs has simplelogger.properties, file an issue and have that fixed. I'd rather see Maven issue a warning, if that is possible, indicating the problem.