I was able to create an App Clip running the Flutter demo by opening ios/Runner.xcworkspace in Xcode 12 and manually adding the target. This is not for the faint of heart and requires some Xcode knowledge to pull off.

Open ios/Runner.xcworkspace
Open the Project settings and hit the + to add a new target
Add an App Clip Target
Interface: Storyboard, Life Cycle: UI App Delegate
When prompted, hit Activate.
Delete the newly created AppDelegate.swift, ViewController.swift, Main.storyboard, Assets.xcassets, LaunchScreen.storyboard
Open Project (not Target!) settings > Info > Deployment Configurations. Base the new App Clip target on the same configurations as your Flutter Runner target. This will give them access to all the Flutter build settings (build number from your pubspec.yaml, etc). So "None" will become either "Debug" or "Release". Set the iOS Deployment Target to 13 (I couldn't get this working on < 13).
Open the App Clip entitlements file. Add the App Clip Associated Domains.
Compile/embed your exiting Runner Swift files and assets into both Runner and the new App Clip target by setting the membership of each of the following files:
AppDelegate.swift, ViewController.swift, Main.storyboard, Assets.xcassets, LaunchScreen.storyboard

etc
Open the App Clip Info.plist. Set Build version string (short) to $(FLUTTER_BUILD_NAME) and Bundle version to $(FLUTTER_BUILD_NUMBER). These need to match between the app and app clip target.
Create a new entitlements file for your Runner app. Selecting the Runner group, File > New > File... Property List
Call it Runner.entitlements (the entitlements extension is important) and add it to the Runner target.
Add the same Associated Domains you added to the App Clip entitlements file. DO NOT add the Parent Application Identifiers.
Open up your Runner target build settings. Set Code Signing Entitlements to the path of the Runner.entitlements file you just made, like Runner/Runner.entitlements.
Open up your App Clip target build settings. Set iOS Deployment Target to iOS 13.0 (or just delete the setting to inherit).
Still in your App Clip target build settings, in Framework Search Paths add $(inherited) and $(PROJECT_DIR)/Flutter in order so it can find the Flutter framework.
Still in your App Clip target build settings, set Objective-C Bridging Header to Runner/Runner-Bridging-Header.h.
Now go to your App Clip target Build Phases tab. Add a New Run Script Phase.
Drag it it so it's right below Dependencies, and paste the following (this matches the build phase in your Runner target).

/bin/sh "$FLUTTER_ROOT/packages/flutter_tools/bin/xcode_backend.sh" build

This will compile your Dart code. This should only happen once when you build your project since the back end will cache the results.

Make another New Run Script Phase. Drag it so it's below Copy Bundle Resources

/bin/sh "$FLUTTER_ROOT/packages/flutter_tools/bin/xcode_backend.sh" embed_and_thin

This will embed your Dart code and the Flutter engine into the App Clip bundle.

Run the App Clip scheme, targeting a iOS 14 device.

And it worked! Note the "Powered by" banner at the top.

Caveats

I make no guarantee of this working for your project, it's just a proof of concept to get you started. Please don't @ me to fix any linker errors, build setting problems, etc. 🙂
Obviously this is all manual, and ideally Flutter tooling would do all this for you.
I wasn't able to connect to the observatory, possibly because an entitlement is missing?
This will embed your entire app into the App Clip. You'll need to figure out the right entrypoint (and create a separate AppDelegate for each target, don't share them). It needs to stay under 10MB per Apple's requirements.
This could potentially be solved by embedding two Flutter add-to-app modules into a host app clip target?
I didn't have any plugins. Hopefully it would be pretty easy to add the new target to your ios/Podfile but I didn't try, maybe (in master) something like:

project 'RunnerAppClip', {
  'Debug' => :debug,
  'Profile' => :release,
  'Release' => :release,
}
...
target 'Runner' do
  flutter_install_all_ios_pods File.dirname(File.realpath(__FILE__))
  target 'RunnerAppClip' do
    inherit! :search_paths
  end
end

Here's a zipped up version of that ios directory so you can open the Xcode project yourself and drop into a newly created flutter create test_appclip demo project. You'll need to change the signing team.
ios.zip

Support app clips on iOS 14 #60029

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