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There are two different classes of timeout in the plugin. Timeout for fetch is governed by the setting in the UI. Timeout for operations which are not fetch are fixed at 10 minutes, at least in one or more cases I've detected. Since fetch is the primary network operation which may be slow, and non-fetch operations are almost entirely local operations, the timeout setting on fetch has been a reasonable heuristic.
Is there any way you can test my theory that the "git submodule" command is blocking on an authentication prompt? For example, can you see if your git server is sending lots of data to the client while that command is blocked? If the server is sending lots of data, then it is not an authentication prompt which is blocking.
Are the submodule repositories expected to take a long time to clone (because they are large)?