Adding a log4j2 configuration via -Dlog4j.configurationFile=/home/henrik/.minecraft/logs.xml allows me to successfully configure log output. So seems the problem is in default log4j2 configuration.
This is the log4j2 logs.xml file I used:
<?xml version="1.0" encoding="UTF-8"?>
<Configuration status="debug">
<Appenders>
<Console name="Console" target="SYSTEM_OUT">
<PatternLayout pattern="%d{HH:mm:ss.SSS} [%t] %-5level %logger{36} - %msg%n"/>
</Console>
</Appenders>
<Loggers>
<Root level="trace">
<AppenderRef ref="Console"/>
</Root>
</Loggers>
</Configuration>
Note: No idea what that log format really means and likely not correct for Minecraft. Only copy-pasted from log4j2 example to see if it could be done. But with that there is log output on the console.