How to reproduce:
1. Open the attached 'EmptyProjectViaScript.zip' project
2. Change Target SDK to Simulator SDK in Player Settings
3. Press BuildMenu > Build in the Menu bar to build Xcode project
4. Open the Xcode project and notice that libiPhone-lib.dylib is present in the Libraries folder
5. Change Target SDK to Device SDK in Player Settings
6. Press BuildMenu > Build in the Menu bar to append the existing build folder

Expected result: The Xcode project contains libiPhone-lib.a in the Libraries folder and the Xcode project builds successfully
Actual result: The Xcode project contains libiPhone-lib.dylib in the Libraries folder and the Xcode project fails to build

Reproducible with: 2018.4.26f1, 2019.4.9f1, 2020.1.4f1, 2020.2.0a21

Notes:
- A screenshot of the error is attached in Edit
- Append flag does not appear when building through menu bar
- This only happens when building Simulator first, then Device. It doesn't happen in the other direction
- This issue is related to 1216005 which was fixed, but the build keeps failing the same way when building through BuildPipeline.BuildPlayer, and while using BuildOptions.AcceptExternalModificationsToPlayer. After further investigation, it was decided to create a new bug report