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Update for the scenario I was looking at: It turns out the job was configured to use "Repository / Name" of something specific to the plan. Once I reset it to "origin" it got past this problem. So, a work-around for people experiencing this problem may be to limit yourself to a "Repository / Name" of "origin"...
I still think this is a real problem, in that if you do configure "Repository / Name", then submodules with relative URL break, but at least it isn't critical for us any more...