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Через безопасный Kotlin DSL:

import org.jetbrains.dokka.base.DokkaBase
import org.jetbrains.dokka.gradle.DokkaTask
import org.jetbrains.dokka.base.DokkaBaseConfiguration

buildscript {
    dependencies {
        classpath("org.jetbrains.dokka:dokka-base:1.8.20")
    }
}

tasks.withType<DokkaTask>().configureEach {
    pluginConfiguration<DokkaBase, DokkaBaseConfiguration> {
        customAssets = listOf(file("my-image.png"))
        customStyleSheets = listOf(file("my-styles.css"))
        footerMessage = "(c) 2022 MyOrg"
        separateInheritedMembers = false
        templatesDir = file("dokka/templates")
        mergeImplicitExpectActualDeclarations = false
    }
}

Через JSON:

import org.jetbrains.dokka.gradle.DokkaTask

tasks.withType<DokkaTask>().configureEach {
    val dokkaBaseConfiguration = """
    {
      "customAssets": ["${file("assets/my-image.png")}"],
      "customStyleSheets": ["${file("assets/my-styles.css")}"],
      "footerMessage": "(c) 2022 MyOrg",
      "separateInheritedMembers": false,
      "templatesDir": "${file("dokka/templates")}",
      "mergeImplicitExpectActualDeclarations": false
    }
    """
    pluginsMapConfiguration.set(
        mapOf(
            // fully qualified plugin name to json configuration
            "org.jetbrains.dokka.base.DokkaBase" to dokkaBaseConfiguration
        )
    )
}

import org.jetbrains.dokka.gradle.DokkaTask

tasks.withType(DokkaTask.class) {
    String dokkaBaseConfiguration = """
    {
      "customAssets": ["${file("assets/my-image.png")}"],
      "customStyleSheets": ["${file("assets/my-styles.css")}"],
      "footerMessage": "(c) 2022 MyOrg"
      "separateInheritedMembers": false,
      "templatesDir": "${file("dokka/templates")}",
      "mergeImplicitExpectActualDeclarations": false
    }
    """
    pluginsMapConfiguration.set(
            // fully qualified plugin name to json configuration
            ["org.jetbrains.dokka.base.DokkaBase": dokkaBaseConfiguration]
    )
}

<plugin>
    <groupId>org.jetbrains.dokka</groupId>
    <artifactId>dokka-maven-plugin</artifactId>
    ...
    <configuration>
        <pluginsConfiguration>
            <!-- Fully qualified plugin name -->
            <org.jetbrains.dokka.base.DokkaBase>
                <!-- Options by name -->
                <customAssets>
                    <asset>${project.basedir}/my-image.png</asset>
                </customAssets>
                <customStyleSheets>
                    <stylesheet>${project.basedir}/my-styles.css</stylesheet>
                </customStyleSheets>
                <footerMessage>(c) MyOrg 2022 Maven</footerMessage>
                <separateInheritedMembers>false</separateInheritedMembers>
                <templatesDir>${project.basedir}/dokka/templates</templatesDir>
                <mergeImplicitExpectActualDeclarations>false</mergeImplicitExpectActualDeclarations>
            </org.jetbrains.dokka.base.DokkaBase>
        </pluginsConfiguration>
    </configuration>
</plugin>

Через параметры командной строки:

java -jar dokka-cli-1.8.20.jar \
     ...
     -pluginsConfiguration "org.jetbrains.dokka.base.DokkaBase={\"customAssets\": [\"my-image.png\"], \"customStyleSheets\": [\"my-styles.css\"], \"footerMessage\": \"(c) 2022 MyOrg\", \"separateInheritedMembers\": false, \"templatesDir\": \"dokka/templates\", \"mergeImplicitExpectActualDeclarations\": false}
"

Через конфигурацию JSON:

{
  "moduleName": "Dokka Example",
  "pluginsConfiguration": [
    {
      "fqPluginName": "org.jetbrains.dokka.base.DokkaBase",
      "serializationFormat": "JSON",
      "values": "{\"customAssets\": [\"my-image.png\"], \"customStyleSheets\": [\"my-styles.css\"], \"footerMessage\": \"(c) 2022 MyOrg\", \"separateInheritedMembers\": false, \"templatesDir\": \"dokka/templates\", \"mergeImplicitExpectActualDeclarations\": false}"
    }
  ]
}