Android: Default FirebaseApp is not initialized in this process error with AGP 3.3.0

Question

I recently updated to Gradle Plugin 3.3.0 with Android Studio 3.3 and I'm getting this error:

io.reactivex.exceptions.OnErrorNotImplementedException: Default FirebaseApp is not initialized in this process <package-name>. Make sure to call FirebaseApp.initializeApp(Context) first.
    at io.reactivex.internal.functions.Functions$OnErrorMissingConsumer.accept(Functions.java:704)

However, it was working fine with AGP 3.2.0

Rest of my configuration is as follows:

Top level build.gradle file:

buildscript {
    ...
    ext.kotlin_version = '1.3.11'
    ext.firebase_core = "16.0.6"
    ext.firebase_messaging = "17.3.4"
    ext.google_services_plugin_version = "4.1.0"

    repositories {
        google()
        jcenter()
    }
    dependencies {
        classpath 'com.android.tools.build:gradle:3.3.0'
        ...
        classpath "com.google.gms:google-services:$google_services_plugin_version" // google-services plugin

        // NOTE: Do not place your application dependencies here; they belong
        // in the individual module build.gradle files
    }
}

allprojects {
    ...
}

...

App build.gradle file:

apply plugin: 'com.android.application'
apply plugin: 'kotlin-android'
apply plugin: 'kotlin-kapt'
apply plugin: 'kotlin-android-extensions'
apply plugin: "androidx.navigation.safeargs"

android {
    ...
}

configurations {
    ...
}

dependencies {

    ...

    //firebase
    implementation "com.google.firebase:firebase-core:$firebase_core"
    implementation "com.google.firebase:firebase-messaging:$firebase_messaging"

    ...
}

apply plugin: 'com.google.gms.google-services'

It seems AGP 3.3.0 is incompatible with these Firebase versions. What can I do to resolve this issue? I updated AGP 3.3.0 because I want to use R8 to resolve an proguard issue.