Unrecognized manifest key 'applications'. warning for Google Chrome

You probably want to generate separate manifest files even if everything else is unchanged. After all, the docs state:

applications. Only supported in Gecko.

My recommendation is a build script that copies over the files and the correct manifest for each version (or dynamically generates the correct manifest if you want fancy).

Running 68.0b13 (64-bit), I just deleted the "applications" key and body

//  "applications": {
//      "gecko": {
//          "strict_min_version": "58.0a1"
//      }
//  },

and it works fine without it.

Documentation says:

Note that the ability to develop and debug WebExtensions that don't include an ID is new in Firefox 48. If you need to use an earlier version of Firefox, then you must use the applications key to set an ID explicitly.

My interpretation of that is that the "application" key is NOT necessary for >= Firefox 48.