I just experienced the same issue and found the fix, at least, for me:
I added the UISceneConfigurations key (inside the UIApplicationSceneManifest dictionary) and its value as an empty dictionary, like this:
<key>UIApplicationSceneManifest</key>
<dict>
<key>UIApplicationSupportsMultipleScenes</key>
<true/>
<key>UISceneConfigurations</key>
<dict/>
</dict>
Note, if your app does not support multiple scenes (i.e. multiple windows or screens), then this is sufficient (and may avoid a strange black screen!):
<key>UIApplicationSceneManifest</key>
<dict>
<key>UISceneConfigurations</key>
<dict/>
</dict>

It compiled and ran successfully without the warning in the debug console, and also automatically removed this key from the project.pbxproj file:

I hope it helps.