I managed to do this by not using Prerender at all but creating AWS Lambda function that:
Configure new origin (new lambda function) and behaviour (map /user/* requests to this new origin). Be sure to use "HTTPS only" Origin Protocol Policy for the origin, as API Gateway is only HTTPS, redirect here will cause the hostname to change.
(If you by accident used the redirect, then you will need to Invalidate "/*" as due to some CloudFront bug the configuration change will not help ; I spent multiple hours debugging this last night)