Figured out the issue.

In order to manage Webhooks, the branch job must have:
a. run at least once
b. contain at least one scm checkout

In my simple testing neither of those cases were true, leading me to go 
round in circles for awhile :)
I suspect the request to manage from the branch source plugin will come too 
early for these conditions to be met.
It might happen eventually (on project re-configuration, or through the 
"re-register all hooks" button) but it's not too intuitive.

A better way of detecting SCMs than the WorkflowJob getSCMs would be nice, 
but I do understand the need to cover hugely complex cases where a simple 
resolution wouldn't apply.
At least now I know, and can come up with workarounds that suit.

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