I am confused on your description of your setup. I have 3 hubs so I have a Maker API instance for each. In my case, it added an "_" to the 2nd instance I setup and a "__" to the 3rd instance automatically. What confuses me about your description is that you are talking about the underscores being added for each node. You should only be seeing the webhook information in the single Config Node that you have per instance of Maker API. When adding any of the Hubitat nodes to your flow, you simply choose that Server which will then give you a list of your devices you have allowed in Maker API.
This is the Config Node for the 3rd instance of Maker API that I setup. Note the 2 underscores at end.
When I want to add a Device Node to a flow for a device on that hub, I just choose the existing Server and the select device from drop-down below it.
It sounds like you are trying to create a different server for every Hubitat node you create but that is not necessary.
Am I completely misunderstanding what you have done?