Hi,
I'm a developer at RainMachine and I remember something similar was mentioned in a meeting. We've contacted Flume to understand what can be done for a better integration between RainMachine and Flume but, if I remember right, you can't set anything via Flume API (thresholds or alerts). What we added recently is the API call to retrieve flow meter counters and also be able to ingest flow meter counters from an external service. This is described here: https://rainmachine.docs.apiary.io/#reference/watering/wateringflowmeter
This probably won't help you directly with what you want to do but might help you in your integration.