For now, I've had to set the mod to "Global Overcast" and to use the vanilla weather system (in turn abiding by the toggledownfall rule).

Would be nice if you could support this mod.

AgriCraft uses the vanilla checks to test if it is raining, so it should pick up any mod that sets the downfall to true. Also, the irrigation system in 1.10.2 is still WIP, so there might be other changes to the system that affect this issue.