Visible through buildcraft oil: http://i.imgur.com/2XUJqmt.png

Yeah definately related, the issue is mostly due to the fact that I use my own custom particle system that hooks into forges world render post event, I'll probably have a look at this issue again once force is at 1.8.8 and I update, vanilla render code might be in a better state for me to fix this in an elegant way at that point.

tornadoes also pick up buildcraft oil

Wouldn't the clouds being visible through the water and oil blocks be due to alpha rendering? I know there are a couple of other mods that if you look through water, or certain transparent blocks, the object/thing disappears.

This issue is still present in the latest update for 1.12.2

My new beta builds are using the old hook that works better with translucent blocks, not perfect but better.