Unfortunately, there have been no Factorio updates that alleviate this issue, or provide any solution.
The main problem is how furnace recipes have been changed. It used to be that you could recycle a chain of random items without emptying the machine, so long as it had empty slots. This changed at some point in development (around 0.15, 0.16, or 0.17) to where the machine would just stop working if the previous recipe didn't match, and the output slots were not empty. The other slots are only used if the recipe has that many ingredients.
This means you have to empty the machine before it can process another recipe. Meaning the fluids have to be ejected as well, and they will always be ejected to the first slot. Meaning, a pipe that has the fluid from the old recipe, will prevent the fluid from the new recipe from being ejected from the machine. Meaning that the machine stops working.
There's no way to manually assign output pipes, at least, not as far as I can tell. Pretty sure they didn't implement GDIW into base game, considering how the Oil Refinery still works. Which means... there's still no vanilla solution to the issue. You either void the fluids, or find another mod that "sort" fluids.
I know that a pump will forcibly empty the pipe behind it, leaving it empty for the next recipe. But then you have to find some way to empty the pump, without simply kicking the can further down the road. There needs to be a fluid sorter to make this work properly.
EDIT: I'm also sorry that I never came back to fix this issue. The only viable solution still seems like a lot of work, for not a lot of gain (especially considering my primary purpose for the mod)