EAS update commands breaking app.json with duplicate entries

### Build/Submit details page URL

_No response_

### Summary

I'm trying to run `eas update:configure`/other eas commands to create a preview on PRs. It keeps editing my `app.json` file to add duplicate entries, which is causing the API request to fail and no build is created.

```
Manifest Validation Error:
ios.associatedDomains:should NOT have duplicate items (items ## 0 and 1 are identical)
android.intentFilters:should NOT have duplicate items (items ## 0 and 1 are identical)
This is likely a problem with your app.json, or app.config.js
Request ID: 8dac6586-207d-4872-be0a-003805b5a08c
```

It duplicates the permissions

and associated domains

I have no idea why it generates this diff. I can't find anything online about it either.

### Managed or bare?

managed

### Environment

```

expo-env-info 1.3.4 environment info:
System:
OS: macOS 15.5
Shell: 5.9 - /bin/zsh
Binaries:
Node: 20.19.3 - ~/.nvm/versions/node/v20.19.3/bin/node
Yarn: 1.22.22 - ~/projects/happyspree-fe/node_modules/.bin/yarn
npm: 10.8.2 - ~/.nvm/versions/node/v20.19.3/bin/npm
Managers:
CocoaPods: 1.16.2 - /Users/maxjohansen/.rvm/gems/ruby-3.3.1/bin/pod
SDKs:
iOS SDK:
Platforms: DriverKit 24.2, iOS 18.2, macOS 15.2, tvOS 18.2, visionOS 2.2, watchOS 11.2
IDEs:
Android Studio: 2024.2 AI-242.23726.103.2422.13016713
Xcode: 16.2/16C5032a - /usr/bin/xcodebuild
npmPackages:
expo: ^52.0.0 => 52.0.37
expo-router: ^4.0.17 => 4.0.17
expo-updates: ~0.27.4 => 0.27.4
react: 18.3.1 => 18.3.1
react-dom: 18.3.1 => 18.3.1
react-native: 0.76.7 => 0.76.7
react-native-web: ~0.19.13 => 0.19.13
npmGlobalPackages:
eas-cli: 16.13.3
Expo Workflow: bare

```

### Error output

_No response_

### Reproducible demo or steps to reproduce from a blank project

N/A