In the QnA Maker Connector you can only specify one subscription key in the connector module itself.
In the actions of the module, I did not find a possibility to define a different subscription key. This means, that in your environment you can only connect to exactly one QnA Maker Resource on Azure.
But if you have knowledge bases that are linked to different QnA Maker resources, then you have no possibility to select between different QnA Maker services.
If I dont misunderstand something, then my proposal is, to move the definition of the subscription key from the connector site property to a (or the) actions of the module. Do you think you can implement this change?