Now I'm really pissed about itch.io not saving my draft. I've lost twice my lengthy answer...
You're mostly right in your observations, with some additions.
Safe morale loss basically adds and extra worker to industry in order to prevent production stalling in case the industry production was decreased due to loss of morale. Unfortunately it's poorly documented on the user side, I might have to extend the tutorial on this.
Optimize Industry used to be called Maximize Industry, thought that's not 100% accurate either. Renaming it though I might have inadvertently reversed the meaning. What it does is that when it's enabled and the current building has more than 1 turn left then instead of distributing industry workers so that they are just enough to finish in the estimated number of turns, it will use the maximum of workers. When it's the buildings last turn, regardless of this option it will use just enough workers to finish (otherwise the extra work is simply wasted).
If the priority of something is 0 it won't get workers unless the workers really have nothing to do. Thus the use stored food option works as intended. Also if a resources store if full it will decrement its workers even if it's set to "Fill All".
If you don't have anything in the industry queue, it will still fill up the industry workers according to priorities, because that production is converted into credits. So that is also intended.
As for the buttons instead of checkboxes, on small screens checkboxes are harder to hit (at least the default ones from libgdx). Also I already had this logic on the setup screen where you start the game so I kept it the same. Basically if the buttons says "enable", the feature is disabled and vice-versa.
If you have more questions/suggestions, feel free to ask.