Four different ciphers sit behind this generator, and only one of them makes a puzzle that stays hard across a whole book. Understanding the difference before you build fifty pages is the single most useful thing to know about the tool, because two of the four use the same key every time they run.
A random substitution assigns each letter of the alphabet a different stand-in, freshly shuffled for every puzzle, so solvers work from letter frequency, word shapes and repeated patterns. A Caesar shift moves the whole alphabet along by a fixed number of places. Atbash flips the alphabet end to end, so A becomes Z and B becomes Y. The reverse option turns the text back to front instead of encoding the letters at all.
Difficulty controls how much of the key you hand over, and the amounts are more generous than most people expect. Easy reveals about a third of the alphabet, roughly nine letters. Medium reveals about a fifth, roughly six. Hard still gives two. There is no setting that provides nothing, which matters if you are aiming at experienced solvers who want the grid bare.
Random substitution, in almost every case. It is the only one of the four that generates a new key for each puzzle, so every page presents a genuinely fresh problem. The other three work better as occasional variety pages than as the backbone of a collection.
Because it leaves the letters untouched and only changes their order, so the words are readable as soon as you look at them backwards. It offers no substitution to deduce and no key to recover.
Easy reveals about a third of the alphabet and medium about a fifth, which works out at roughly nine and six letters. Hard always reveals exactly two. No setting produces a puzzle with no assistance at all.