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I figured out the root cause of this in my installation. The problem is that the initial checkout is using the credentials plugin but the submodule checkout is using the default user credentials defined in `~/.ssh/config`. If there is not `config` then SSH by default will look for `~/.ssh/id_rsa` as the private key for the connection. My jenkins system user has default credentials in `~/.ssh/id_rsa` and so I had to give the user using those credentials access to the submodule project with read permissions.
Hopefully that was clear. Essentially, the git plugin claims it is reusing credentials plugin for the submodule check out but it is actually not using it at all. I'll try to dig through the source to point out where it is doing this.