I’m actively using that approach in my projects and I saw no issue in terms of detections so I recommend reviewing your steps and making sure everything is done properly.
If you have only the .onnx file for your network and not the weights file, you need to use an onnx parser. I don’t have any experience with that, but I can give you an example of a similar approach.
Please refer to this example to parse onnx and make changes:
Or you can implement a custom bbox parser for deepstream.