Workarounds

• It's not a problem using Gradle 5, it seems
• You can add a hard exclude of this optional dependency like so (if that's an option for you):

    implementation(group: 'org.dom4j', name: 'dom4j', version: "2.1.3") {
        exclude group: "pull-parser", module: "pull-parser"
    }

(Gradle, Groovy DSL)

Confirming that this issue first appeared in Gradle 6.0.

To exclude all optional dependencies of dom4j:

compile(group: 'org.dom4j', name: 'dom4j', version: '2.1.3') {
	exclude module: 'pull-parser'
	exclude module: 'jaxen'
	exclude module: 'xpp3'
	exclude module: 'xsdlib'
	exclude module: 'stax-api'
	exclude module: 'jaxb-api'
}

excludes are actually not the semantically correct way to fix invalid metadata.
That's more symptom treatment, like calling Thread.sleep to "fix" multi-threading issues or SwingUtilities.invokeLater to "fix" GUI issues.
Instead component metadata rules should be the tool of choice.
As all dependencies are optional, a simple one would be:

dependencies {
   components {
       withModule('org.dom4j:dom4j', ClearDependencies)
   }
}

class ClearDependencies implements ComponentMetadataRule {
   void execute(ComponentMetadataContext context) {
       context.details.allVariants { withDependencies { clear() } }
   }
}

(c) melix from gradle/gradle#13656 (comment)

I have try and got an error at runtime

2022-08-01 08:36:09.183 6826-6826/com.xxx.dev E/AndroidRuntime: FATAL EXCEPTION: main Process: com.xxx.dev, PID: 6826 java.lang.NoClassDefFoundError: Failed resolution of: Lorg/jaxen/dom4j/Dom4jXPath; at org.dom4j.xpath.DefaultXPath.parse(DefaultXPath.java:353) at org.dom4j.xpath.DefaultXPath.<init>(DefaultXPath.java:59) at org.dom4j.DocumentFactory.createXPath(DocumentFactory.java:222) at org.dom4j.tree.AbstractNode.createXPath(AbstractNode.java:202) at org.dom4j.tree.AbstractNode.selectNodes(AbstractNode.java:159) at xxx(my app package) at xxx(my app package) at xxx(my app package) at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33) at kotlinx.coroutines.DispatchedTask.run(DispatchedTask.kt:106) at kotlinx.coroutines.internal.LimitedDispatcher.run(LimitedDispatcher.kt:42) at kotlinx.coroutines.scheduling.TaskImpl.run(Tasks.kt:95) at kotlinx.coroutines.scheduling.CoroutineScheduler.runSafely(CoroutineScheduler.kt:570) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.executeTask(CoroutineScheduler.kt:749) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.runWorker(CoroutineScheduler.kt:677) at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.run(CoroutineScheduler.kt:664) Suppressed: kotlinx.coroutines.DiagnosticCoroutineContextException: [StandaloneCoroutine{Cancelling}@48d11a8, Dispatchers.Main.immediate] Caused by: java.lang.ClassNotFoundException: Didn't find class "org.jaxen.dom4j.Dom4jXPath" on path: DexPathList[[zip file "/data/app/~~iRsRncGn8L063hNDpVm64A==/xxx-PpfNVzHq5gt0ms5r9BNdZQ==/base.apk"],nativeLibraryDirectories=[/data/app/~~iRsRncGn8L063hNDpVm64A==/xxx-PpfNVzHq5gt0ms5r9BNdZQ==/lib/arm64, /data/app/~~iRsRncGn8L063hNDpVm64A==/xxx-PpfNVzHq5gt0ms5r9BNdZQ==/base.apk!/lib/arm64-v8a, /system/lib64, /system_ext/lib64]] at dalvik.system.BaseDexClassLoader.findClass(BaseDexClassLoader.java:259) at java.lang.ClassLoader.loadClass(ClassLoader.java:379) at java.lang.ClassLoader.loadClass(ClassLoader.java:312) ... 16 more

They are optional dependencies, not unnecessary dependencies. If you use the part that needs that dependency, you also need the dependency.

The quick and easy way is to add it as runtimeOnly dependency.
The semantically correct way would be to - either in the same or another component metadata rule - add a variant for that use-case and then depend on that variant.