The larger issue is in javas dependency system are built with dependencies on these libraries, so if there is no commons logging (or bridge, ala slf4j), then the program won't run.
There are a few other techinical traps with the jvm, like using system.out logging can cause issues with threaded code, or having one giant static logger being imported all over the place conveniently (this is before inversion-of-control became the dominant paradigm) had a few shortcomings, especially as programs grew. Ultimately, though, if you were going to use some third party libraries or app servers, you were almost certainly going to get pulled into the commons-logging vortex, which means you're now configuring that AND your homespun logger.
There is also the case for things like SOLR, where it might be just being used out of the box, but the distribution includes the affected JARs, even if you're just posting and retrieving documents with a python script doing print-logging.
Honestly, I didn't even know log4j2 was a thing, I've moved as much over to slf4j/logback as I could ages ago because of the madness of the JDK logging ecosystem.