Guess I have understand both the difference (please correct me if my understanding is incorrect), 
For use_frameworks! please read here as it has already describe what it's for. 
For use_native_modules!, it's actually being use in React Native 0.60 and above for auto-linking. With the command specified in podfile, all the new dependency appended to project do not require developer to append new dependency's podspec into podfile. It will link automatically when you run pod install command.
I have been appending all the podspecs myself ever since I upgraded to RN0.60  
Sample podfile
platform :ios, '9.0'
require_relative '../node_modules/@react-native-community/cli-platform-ios/native_modules'
target 'example' do
  # Pods for example
  pod 'FBLazyVector', :path => "../node_modules/react-native/Libraries/FBLazyVector"
  pod 'FBReactNativeSpec', :path => "../node_modules/react-native/Libraries/FBReactNativeSpec"
  pod 'RCTRequired', :path => "../node_modules/react-native/Libraries/RCTRequired"
  pod 'RCTTypeSafety', :path => "../node_modules/react-native/Libraries/TypeSafety"
  pod 'React', :path => '../node_modules/react-native/'
  pod 'React-Core', :path => '../node_modules/react-native/'
  pod 'React-CoreModules', :path => '../node_modules/react-native/React/CoreModules'
  pod 'React-Core/DevSupport', :path => '../node_modules/react-native/'
  pod 'React-RCTActionSheet', :path => '../node_modules/react-native/Libraries/ActionSheetIOS'
  pod 'React-RCTAnimation', :path => '../node_modules/react-native/Libraries/NativeAnimation'
  pod 'React-RCTBlob', :path => '../node_modules/react-native/Libraries/Blob'
  pod 'React-RCTImage', :path => '../node_modules/react-native/Libraries/Image'
  pod 'React-RCTLinking', :path => '../node_modules/react-native/Libraries/LinkingIOS'
  pod 'React-RCTNetwork', :path => '../node_modules/react-native/Libraries/Network'
  pod 'React-RCTSettings', :path => '../node_modules/react-native/Libraries/Settings'
  pod 'React-RCTText', :path => '../node_modules/react-native/Libraries/Text'
  pod 'React-RCTVibration', :path => '../node_modules/react-native/Libraries/Vibration'
  pod 'React-Core/RCTWebSocket', :path => '../node_modules/react-native/'
  pod 'React-cxxreact', :path => '../node_modules/react-native/ReactCommon/cxxreact'
  pod 'React-jsi', :path => '../node_modules/react-native/ReactCommon/jsi'
  pod 'React-jsiexecutor', :path => '../node_modules/react-native/ReactCommon/jsiexecutor'
  pod 'React-jsinspector', :path => '../node_modules/react-native/ReactCommon/jsinspector'
  pod 'ReactCommon/jscallinvoker', :path => "../node_modules/react-native/ReactCommon"
  pod 'ReactCommon/turbomodule/core', :path => "../node_modules/react-native/ReactCommon"
  pod 'Yoga', :path => '../node_modules/react-native/ReactCommon/yoga'
  pod 'DoubleConversion', :podspec => '../node_modules/react-native/third-party-podspecs/DoubleConversion.podspec'
  pod 'glog', :podspec => '../node_modules/react-native/third-party-podspecs/glog.podspec'
  pod 'Folly', :podspec => '../node_modules/react-native/third-party-podspecs/Folly.podspec'
  target 'exampleTests' do
    inherit! :search_paths
    # Pods for testing
  end
  use_native_modules!
end
target 'example-tvOS' do
  # Pods for example-tvOS
  target 'example-tvOSTests' do
    inherit! :search_paths
    # Pods for testing
  end
end