Is it possible that this could be a separate option/checkbox? This would be something I would be happy to beta test or something. I have this problem constantly and it can be really frustrating to have to make a minimum of 10 clicks (I counted) to cycle through turning the "Software mouse cursor" Off, then click done, then reopen and turn the "Software mouse cursor" back On.
Other suggestions to possibly help reduce the frustration is adding an "Apply" button that doesn't close the f.lux Options window, or a "cycle software mouse cursor" button or effect. Any of these would at least make it easier to manually fix the off/on process rather than having to program an auto-fix.
If you'd like a list of games that require this, I'd be happy to start keeping track and let you know, but it's probably 40% of the games I play.