Fix and refactor scripting subplugin application logic

so warning is not shown when discovery configuration is not populated
fix #KT-31124
refactor code for clarity on the way
also apply scripting subplugin after main plugin to ensure that
configurations are created before scripting is initialized

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KotlinGradlePluginIT.kt

@@ -19,6 +19,7 @@ package org.jetbrains.kotlin.gradle
 import org.gradle.api.logging.LogLevel
 import org.jetbrains.kotlin.gradle.plugin.MULTIPLE_KOTLIN_PLUGINS_LOADED_WARNING
 import org.jetbrains.kotlin.gradle.plugin.MULTIPLE_KOTLIN_PLUGINS_SPECIFIC_PROJECTS_WARNING
+import org.jetbrains.kotlin.gradle.scripting.internal.ScriptingGradleSubplugin
 import org.jetbrains.kotlin.gradle.tasks.USING_JVM_INCREMENTAL_COMPILATION_MESSAGE
 import org.jetbrains.kotlin.gradle.util.*
 import org.junit.Test
@@ -995,4 +996,12 @@ class KotlinGradleIT : BaseGradleIT() {
             assertSuccessful()
         }
     }
+
+    @Test
+    fun testNoScriptingWarning() = with(Project("simpleProject")) {
+        // KT-31124
+        build {
+            assertNotContains(ScriptingGradleSubplugin.MISCONFIGURATION_MESSAGE_SUFFIX)
+        }
+    }
 }