After further testing with my flow sensor connected, I am seeing values from the API jl call as well as with the type=fl parameter. It appears to be working correctly as you stated.
However, even after further testing by manually shorting the sensor pin to ground or by attaching my flow sensor and trying different firmware versions, the counts are still not accurate with 2.1.9(3) as compared to 2.1.9(0).
Let me know if you are not able to re-create this even by manually shorting the sensor pin 20-25 times for a 1 minute station run. If not, then maybe there is a problem with my specific unit (OpenSprinkler 3.2 DC).