Issue title: Linking godot project folder to xcode project breaks C# scripts
 Issue body: ### Godot version

3.3.3

### System information

macOS 11.3 (M1), iPhone SE 2020

### Issue description

Hello everyone,

I'm having problems setting up my xcode development environment following [this description](https://docs.godotengine.org/en/stable/getting_started/workflow/export/exporting_for_ios.html#steps-to-link-a-godot-project-folder-to-xcode) in the godot docs.

What works: I can export my godot project using the iOS template, build it in xcode and run it successfully on my iPhone.

What does not work: To avoid having to re-export the project every time I make a change I want to link my godot project folder into the xcode project as described in the docs (link above). So, I set the `godot_path` in the *.plist, linked my godot project folder and removed the *.pck file. Running the project on my iPhone works, but none of the C# scripts is run. Instead I get this output in xcode:

    testproject_xcode[4277:2005214] **ERROR**: Mono: Core API hash mismatch.
    2021-08-20 09:48:47.463360+0200 testproject_xcode[4277:2005214]    At: modules/mono/mono_gd/gd_mono.cpp:494:_init_godot_api_hashes() - Mono: Core API hash mismatch.
    **ERROR**: Mono: Core API hash mismatch.
       At: modules/mono/mono_gd/gd_mono.cpp:494:_init_godot_api_hashes() - Mono: Core API hash mismatch.
    2021-08-20 09:48:47.464650+0200 testproject_xcode[4277:2005214] Mono: Config attempting to parse: '/private/var/containers/Bundle/Application/ABDCA2AE-7826-4F19-972D-EC6A84635B0F/testproject_xcode.app/data_Godot/Mono/etc/mono/config'.
    2021-08-20 09:48:47.464716+0200 testproject_xcode[4277:2005214] Mono: Config attempting to parse: '/private/var/mobile/Containers/Data/Application/3A1BEBBF-67BF-4B29-8A43-64D652FDC7C2/.mono/config'.
    2021-08-20 09:48:47.537006+0200 testproject_xcode[4277:2005214] **ERROR**: Cannot instance script because the project assembly is not loaded. Script: 'res://Scenes/TestScript.cs'.
    2021-08-20 09:48:47.537062+0200 testproject_xcode[4277:2005214]    At: modules/mono/csharp_script.cpp:2905:can_instance() - Method failed. Returning: __null
    **ERROR**: Cannot instance script because the project assembly is not loaded. Script: 'res://Scenes/TestScript.cs'.
       At: modules/mono/csharp_script.cpp:2905:can_instance() - Method failed. Returning: __null

To see what might be amiss I had a look at the contents of the PCK file (using [GodotPckTool](https://github.com/hhyyrylainen/GodotPckTool)). There are some notable differences between my project folder and the pck contents. For example, in `.mono/assemblies/Debug/` there are a couple more files in the PCK.

I'm not 100% sure if this is a bug, if the documentation is not up to date or if I'm missing something. 

### Steps to reproduce

- Create a godot project with mono
- Create a scene and add a C# script to some node
- Export project using iOS template
- Open exported xcode project
- Remove *.pck file, link godot project folder into xcode project, set 'godot_path'  to that folders name in *.plist (as described [here](https://docs.godotengine.org/en/stable/getting_started/workflow/export/exporting_for_ios.html#steps-to-link-a-godot-project-folder-to-xcode))
- Build and run project an iPhone
- Observe debug outout in xcode

### Minimal reproduction project

_No response_
 Comments: 
 Comment 0: I have the same issue. 
Also, if I do a full export, and then later try to update the pck, with "Export PCK/Zip" the project will not compile in xcode becasue of  the "Core API hash mismatch." error.

{'source': 'GithubIssues', 'repo_name_with_owner': 'godotengine/godot', 'issue_id': 976055304, 'repo_stars': 52996.0}