I think Uranium feels so simple, mostly because I haven't overhauled it.
As for Flourine, it's something I decided quite a while ago NOT to use. Let me go into the history of the mods a little.
One of the first things I started to add as "Complex" production chains were metal processing recipes, including Tungsten, Titanium and Aluminium. Aluminium was supposed to be a lower technology level than Tungsten and Titanium, so I wanted it to be a little more simple to process. It turns out that Titanium is actually the simplest to process, and Aluminium more complex.
I did mostly keep the complexity of Aluminium in there, but there's one key component of the process missing... You're supposed to dissolve Alumina (Aluminium oxide) in Molten Florine, and then Electrolyse the solution.
This would have meant adding Florine to the list of already a significant amount of new resources to the game, Just for processing aluminium, a process
that was supposed to be fairly simple in the mod. I decided from this quite early point in the development, No florine!
I'm not saying that you've come up with a bad idea, I've actually added materials that play a smaller part than Florine would if added now, EG to make the Lithium batteries, I added Lithia water AND Cobalt. Cobalt definitely plays a much larger role in my mods now, and I'm fairly sure Lithia is used for more than just batteries, but, at the moment... Well, there are other mods that add florine, and although I'm not familier with them, Angels and Clowns mods come to mind.
If you want to write a mod that adds Florine to bob's mods, Go for it!
That chart does look pretty complex though. If I ever get the feeling to do another Bob overhaul, I'll probably consider it, it does look like there's some interesting chemical processes in there, and you have really thought it through.
Also, I dig the comment about Chemical Furnace lacking an output pipe. I've come up with several recipes where my first instinct is "Looks like a job for the chemical furnace!... if only it had an output pipe..." Think of this as the difference between them. The chemical furnace is a facility where you heat a solid to become a liquid, and bubble a gas through it... or just add a liquid to a solid as you heat it up, so the output result (after cooling) should be a solid. The chemical plant on the other hand takes fluids from the start, so the product should be a fluid. I know this isn't always the case, like Batteries, or even solid fuel, but as a general rule those also make sense in a chemical plant rather than an assembling machine.