I think I managed to solve it. The FCM plugin uses the gradle file to apply the google-services plugin. What I did:
Comment out these lines in the FCMPlugin.gradle file.
classpath 'com.google.gms:google-services:3.0.0'
apply plugin: com.google.gms.googleservices.GoogleServicesPlugin
Then change the plugin.xml of the FCM plugin to use a different version, in my situation 9.8.0.
<framework src="com.google.firebase:firebase-core:9.8.0" />
<framework src="com.google.firebase:firebase-messaging:9.8.0" />
Now, remove en add the android platform again, so the changes will have affect. The next step is to change the build.gradle file of the android platform folder.
Add this line to the classpath section
classpath 'com.google.gms:google-services:3.1.0'
And add this line below the dependencies, nearly at the bottom of the file
apply plugin: 'com.google.gms.google-services'
And these changes should fix the problems with the version conflicts.