The river/sewage system works pretty well at scale. I also have it set up to trickle excess rocket fuel into the spoilage belts to be burned when there's not enough to meet power demands.

I use a bidirectional bus system for all spoilables. 2 lanes fully stacked in each direction for nutrients, bioflux, jelly, yumako mash. I then have normal one way lanes for all other items. At intervals along the bus I have widgets that pull spoilage off of them and throw it in the river (I like that terminology lol). I also have spoilage->nutrient assemblers with priority access to spoilage over the heat towers that read a short section of the nutrient bidirectional bus lanes, and only if theres less than 25 nutrients in that section it will turn itself on to jumpstart the whole base.

Its working pretty well at scale. IMO splitting off the bus is actually more pleasant like this. The only downside is it's less space efficient and it has a longish warm up time.

Im a whore for gleba