The content of config.jelly looks correct:
<f:checkbox name="useAsBuildDisplayName" checked="${instance.useAsBuildDisplayName}" />

But it seems that the VersionNumberBuilder class is missing this getter method:
public boolean getUseAsBuildDisplayName() {
return this.useAsBuildDisplayName;
}

The checkbox is correctly saved and used in the build but when opening the configuration it is not correctly restored for the form.

I immediately assigned this to cchabanois because he committed this feature (which I really like, by the way).