desktop: Switching to a branch with submodules is not possible

Describe the bug

If GitHub Desktop cloned a repository on a branch without submodules, when attempting to switch to a branch with submodules, GitHub Desktop throws the following error:

fatal: not a git repository: ../.git/modules/<submodule name>
fatal: could not reset submodule index

Additionally, after the attempt, GitHub Desktop creates a .gitmodules file with the following contents:

[submodule "<submodule name>"]
    path = <submodule name>
    url = <submodule url>

The workaround for this issue is to remove the following lines from .git/config before attempting a branch checkout:

[submodule]
    active = .

If a checkout attempt is done before the removal, the workaround won’t work. The submodule won’t get initialized and updated on checkout any more, even after removing those lines and clearing up the leftovers.

Version & OS

Version 2.9.3 (x64) Windows 10 Enterprise, version 1809, build 17763.2114

Steps to reproduce the behavior

1. Create a repository with a default branch set to a branch without any submodules.
2. Create a branch in the repository and add a submodule to it.
3. Checkout this repository with GitHub Desktop. It should checkout the default branch without submodules.
4. Try checking out the submodule branch. GitHub Desktop should throw the error mentioned at the top of this page.

Expected behavior

I believe GitHub Desktop should run git submodule update --init --recursive on every branch checkout and clone. I believe this would guarantee that submodules are always initialized and set to proper commits depending on a given branch.

Actual behavior

GitHub Desktop throws and error and refuses to checkout the branch.

Screenshots

Not possible due to company policy.

Logs

Not possible due to company policy.

Additional context

N/A