Minimal flavor does a few things...
Civs that prefer tundra and/or snow are changed to no longer prefer tundra or snow. No change is made for civs that prefer anything else- desert, plains, hills, forests, etc. Civ specific preferences for north/south and east/west are ignored and everybody's preference for the map edges is reduced by one, for most civs this makes their edge preference -1 so they gain a preference for the map center. Tundra and snow can be replaced with grassland within 3 tiles of the starting plot (simple 7x7 square), the chance is highest adjacent to the start plot, the chance is higher on riverside tiles and plots with resources (or unique features) are skipped.
The smart climate is pretty simple so there are 'bad' cases that can occur. Desert, Tundra and Jungles are evaluated to see if you have civs that prefer them. With 'modifiy selection' on, it starts at -1, so one setting 'less' than where you had it and with 'override selection' it starts with them off. Each civ that has a preference for desert, tundra or jungle will increase the value, how much they increse it depends on how many civs are in the game. Using 'modifiy selection' one civ is normally enough to push the the selection change from -1 to 0 unless you have a lot of civs in your game, two may not be enough to push it from -1 to +1. So if you start with increased deserts but end up with no desert civ using 'modifiy selection' you'll get the default amount of deserts, not reduced. The final value for 'override selection' is a little different, it's quite a bit more precise and uses the actualy settings within the selctions rather than modifing the selection itself. So if you have a desert civ this setting will will calculate the difference in desert threshold between the minimal and maximum settings and adjust it upward by a percentage of that difference, the exact percentage depends on how many desert civs you have compared to how many total civs you have. Tundra and jungles are special cases because they depend so highly on where the land is, not how much of it there is. You can still get fairly large tundra regions even with minimal tundra if the random numbers decide to setup the map the 'right' way. It's unfortunate that FfH and subsequent mods of FfH have decided that deer and beavers only live in the tundra (and dye and sugar require jungles) but there isn't anything I can do about that without hardcoding resource values which I won't do.
The minimal smart climate setting will take any terrain that you turned off and set it to 'reduced' (not minimal) if you have at least one civs that prefers that terrain.
When the smart climate evaluates the continent it's tricky. The first step is to simply look at the percentage of land used by the largest continent, that determines if it needs to increased or decrease plains and deserts. This change is just a modifier of whatever you selected, it will adjust the final threshold by +/- 20%. The second check simply count the land tiles by thse north of the mid point and those south of it. The ratio of north:south controls how much tundra or jungle tempertures can be changed. This is one of those cases where you can look at a map and see things that it is very difficult to explain to the computer. It could be improved to be more intelligent but that would be significantly more complicated and slow things down considerably. In most cases it's good enough so I went with speed
Because I've tried to keep things as 'natural' as possible you will get some cases that completely break all of the rules, or appear to anyway. A large desert in the middle of a massive continent that is pretty well centered on the map will not be in an area cool enough for the 'great plains' to have an effect. The smart climate is working though, where you ended up with a single large desert the map most likely originally had one large desert and a few smaller ones, your 20% reduction to the threshold just condensed it all down to one place. When you have larger deserts you also get fewer desert tiles removed during cleanup when I make sure you never have desert adjacent to grassland. Since these cases are just a few of an infinite (or nearly infinite)number of possible combinations they slip through. If I strenghten the effect of the smart climate desert reduction you'll get no deserts on some maps.
Too many random things in there, try changing your PC clock before you generate your map next time
