I dont know about that flood and drain system as I know fuck all about that type of setup ,Refering to space required for roots that is ...
But as a Plumber that angled pipe wont be a drama due to it can only hold so much water (nute) before it over flows and spills back into your res ...
If it were mine I'd cut the pipe and have it on a slight angle downwards ...
Cheers&Peace
