A DESCRIPTION OF THE PROBLEM :
Maybe I'm wrong, but as of JDK 23, it is not possible to patch a module loaded using a dynamic ModuleLayer.
The --patch-module option only allows patching modules that are available at boot time.
The module API does not offer any function like addPatch().

To handle this case, as a workaround, I am currently patching the java.base module with the following class:
package javapatch.lang.module;

import java.lang.module.ModuleFinder;
import java.lang.module.ModuleReference;
import java.nio.file.Path;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;

import jdk.internal.module.ModulePath;
import jdk.internal.module.ModulePatcher;

public class PatchedModuleFinder {
    public static ModuleFinder of(Map<String, List<String>> patches, Path... entries) {
        // special case zero entries
        if (entries.length == 0) {
            return new ModuleFinder() {
                @Override
                public Optional<ModuleReference> find(String name) {
                    Objects.requireNonNull(name);
                    return Optional.empty();
                }

                @Override
                public Set<ModuleReference> findAll() {
                    return Set.of();
                }
            };
        }

        return ModulePath.of(new ModulePatcher(patches), entries);
    }
}

The function PatchedModuleFinder.of() is a modified copy of ModuleFinder.of(), which takes an additional argument containing the map of patches to apply to the modules found by the finder.
It only instantiates a ModulePatcher and provides it to ModulePath.of().

This patch seems to work (at least for now), and I think adding this static function to ModuleFinder would be a great addition (at least for me), as it would allow configuring a dynamic ModuleLayer with the complete feature set available to the boot layer.

As I'm not familiar with the intricacies of JPMS, there might be a good reason for not allowing patching in a dynamic ModuleLayer.

I hope you will find this simple change worthy of modifying the module API.
Best regards,
Pascal