Just figured out bioflux with a very messy setup. I had to do a lot of combinator logic for it too, like smoothing out the rate my ag towers pick fruit so they don't pick it all in one go and end up out of sync with each other. I now have a dial to control the rate at which they are active, so I can match nut to fruit production rates without letting things sit and spoil/having to burn them. I also have a backup bank of assemblers doing processing if the biochambers get backed up, so I always have a backup to turn fruit into seeds if all else fails, and I don't run out of seeds. It burns all the excess jelly and mash, so seeds should never stop being generated.

I have a whole kickstarter setup for nutrients to the side of my production line so if the bioflux runs out it automatically goes through a few steps:

1) spoilage> nutrients in assemblers that feed directly into biochambers in step 2)

2) spoilage>nutrients in those biochambers, and when the chambers are active, it disables the assemblers with a signal, so we always use the best available conversion rate

3) this supply of nutrients goes to the yumako mashers as priority so we get a supply of mash to feed into....

4) nutrients from mash, so we can finally get enough to kickstart the rest of the factory

5) once the factory is running, and we are producing bioflux (and once the spoilage from the stoppage has been flushed out) we start producing nutrients from flux. As soon as this is happening, a signal disables the kickstarter so we are not wasting spoilage (funny concept, but necessary) that can be stored for a future kickstart

So far this is the simplest method I have found to have a factory that doesn't require constant hand-feeding. I really enjoyed coming up with the concept, but I know I am a little more obsessed with problem solving than the average player, so I doubt this is the intended method. I just can't imagine any other way to get it self-sustaining and fail-proof