Sorry, I cannot reproduce it.
If I create a class from template, and a I add several methods, I have
pretty formated code:

public class ffff {
    
    /** Creates a new instance of ffff */
    public ffff() {
    }

    public void newMethod() {
    }

    public final class InnerClass {
    }
    
}

If it happens to you in some tests, please attach these unit tests.

See ref files of java test suites in org.netbeans.test.java.generating
package.
(Java module functional tests).

Try to generate this:

public class ffff {
    
    /** Creates a new instance of ffff */
    public ffff() {
    }

    public void newMethod() {
    }

    class InnerClass {
        public void innerMethod() {
        }
    }   
}

it seems it is right now, i'm closing it as worksforme

verified

Reorganization of java component