Nikin,
This shouldn't cause any problems with your builds. When you build your Android app, the google services plugin will use only the Firebase project data for the application id (package name) that is currently being built. The the data for other Firebase projects is ignored.
The reason for having all apps in the same json file is to facilitate building multiple related apps from the same codebase. So if you have two flavors of apps defined in your build.gradle, you could build them with slightly different Firebase configurations all stored in that single json file.
Doug