K, I've mocked it up in my creative world and I've solved my problem. Each machine takes 1 retriever, 1 regulator and 2 transposers and then I can guarantee the output of the final regulator will always be balanced. Screenshots are attached
This shows the barrels for the system. You'll see a pipe below and above. These are a bit better hidden in my real world, but essentially it's just a network connected to top/bottom of every barrel.
This shows the side of a system supporting 3 separate machines. Each one has it's retriever, to a pipe, to a transposer, to a pipe, to a regulator, to the final output. The retriever and regulator are both set to pull the same items & both on default configs. The transposer is only there so that it can be blocked off by redstone (More on that w/ image 3). The pipe going up has a restriction pipe on it and essentially ensures that if an incorrect mixture gets pulled by the retrievers it'll get sent back - the transposers here are just to make sure the items only go 1-way here.. You'll also see another transposer on the front-left of the screenshot above a restriction pipe. This was because I found sometimes when I turn off a retriever (more on that) items in transit get stuck in the pipe network cause they can't go to their regulator and they can't get back in their barrel. This lets the overflow get back to storage.
Next you see the redstone. Basically I have a timer at the bottom (You can kinda see it), a redstone wire going up into an AND gate, which is past a NOT gate. The basic result here is that the switch on the block above the transposer both powers the transposer and also cuts power to the AND gate, turning off the retriever so it'll stop pulling items when it's transposer closes.
The regulator will still claim the next item it likes to come by after it is turned off before it gets blocked up by not having a way out (the transposer) which introduces the bad ratios of items getting through. The regulator though will ensure that once that machine is turned back on any excess items which were clogging it's pipes will be released back up it's overflow pipe and the final diamond chest (representing a more complex processing machine) always gets the right ratio of items into it.
For the real thing I'll probably lay out the redstone a bit different & use wireless redstone so I don't have to go down into the machine-room to switch machines, but yeah the concept is what I was after
Only downside I've found to this system is that I still can't have two machines both switched on for the same item at once, but I can at least have multiple machines so long as I choose between them.
Thanks for all the ideas helping me towards this