Looks good to me! Can we just add few tests where we show that this actually overrides options specified in the build files?

Not sure if it's worth the effort, that would significantly increase build times for a feature which should be tested in Gradle itself.

Also (just for my better understanding) how do we know that this will override existing option? Is there a defined order what option (from build files or command line) applies first? Like, are we sure that we will always load options from a build file first, and only then the options from the command line (so that the override is always achieved)?

We know because the convention values of the tasks are set from the extension, and that the overrideXXX methods are using the set method, so it's guaranteed to override. If it wasn't the case that would be a bug.