Dependabot cannot update package because of git_dependency_reference_not_found

### Is there an existing issue for this?

- [X] I have searched the existing issues

### Package ecosystem

Pip

### Package manager version

_No response_

### Language version

python_version = "3.11"

### Manifest location and content before the Dependabot update

./src/Pipfile

[[source]]
name = "pypi"
url = "https://pypi.org/simple"
verify_ssl = true

[packages]
flask = "==3.0.3"
marshmallow = "==3.19.0"
dependency-injector = "==4.42.0"
mypckg = {ref = "mypckg-v1.0.0", git = "git+https://${MY_GH_PAT}@github.com/org/python-packages.git", subdirectory = "src/mypckg"}

[requires]
python_version = "3.11"

### dependabot.yml content

version: 2
registries:
python-packages:
type: git
url: https://github.com
username: x-access-token
password: ${{secrets.MY_GH_PAT}}
updates:
- package-ecosystem: "pip"
directory: "/src"
schedule:
interval: "daily"
open-pull-requests-limit: 0
registries: "*"
insecure-external-code-execution: allow

### Updated dependency

werkzeug

### What you expected to see, versus what you actually saw

I want to see that the dependabot creates a PR with a new version of werkzeug, but instead of dependabot pipelines are failed with this error:
Dependabot encountered '1' error(s) during execution, please check the logs for more details.
+-------------------------------------------+
| Dependencies failed to update |
+----------+--------------------------------+
| werkzeug | git_dependencies_not_reachable |
+----------+--------------------------------+

### Native package manager behavior

_No response_

### Images of the diff or a link to the PR, issue, or logs

_No response_

### Smallest manifest that reproduces the issue

_No response_

Start by reproducing the werkzeug update with src/Pipfile and dependabot.yml, paying particular attention to the mypckg git dependency and its ref. Then inspect the Pip ecosystem handling of git dependencies and compare the reported git_dependency_reference_not_found and git_dependencies_not_reachable errors. Done means Dependabot can create the werkzeug update PR without the unrelated git dependency blocking the run.

Written by the indexing model from the issue text.