I honestly doubt those items are supposed to random at all since so far, all the important items have been fixed on specific floors and chests. I don't think they would make the game filled with such random element which allows you to get past the limit cap at that point in game. Why would they go to the extent to specifically place the 4th wave upgrade at the last floor of the final dungeon and then let you have a chance randomly elsewhere, that would just be bad design. Well, in kazuma's case, I don' know how and have no explanation. Maybe his game is bugged somewhere or something I guess.
Haha, I would certainly like to see them do that just for the lolz, but if it's still doable then I would probably try to play on that setting as well.
If you don't want to bother remembering which to answer yes, just select yes for all of them. You'll skip the prologue and tutorial which takes the most of your time. The other 2 will explain to you regarding the interface on the main map and whatnot but those can be skipped by left clicking so yes all the way should be safest. I'm currently on chapter 3