Been here about a year and a half; after the internal Rachio engineers, the Cypress engineers (who make the wireless chip inside), and a contracted engineering group looked like they couldn’t get it resolved, I’m pretty confident they’re not sure what the issue really is and Apple is helping diagnose it.
In their defense, they did try quite a few things, including using Apple’s SDK directly instead of the Cypress SDK (which I assume would then interface with the Apple HomeKit SDK). They have released 2 (I think?) beta firmwares in the last 10 months; the first bricked at least one controller (Macsterguy’s, which Rachio replaced) and the second seems to have fixed it for some (the originator of this thread, Macsterguy) but definitely not for all (myself and most of the people still commenting regularly at the very least).
Official updates (and a much shorter thread as a result as only staff can post in it) is found here: The Official HomeKit Updates Thread - #31 by dane