Hello there.
This is a menu that is using default window classes to draw themselves, so anything you can use to modify the default menu windows will also affect these windows. There are no plugin params to make the windows transparent, or a solid color, but it will use whatever your system graphic is, so it will match the other default windows in your menus.
I don't currently have a feature to distribute items on level up, and that is a good suggestion so I will see if I can add that in later. Until that time, it could technically be possible to do so via a common event, as all of the current levels are stored in $gameParty._craftlevels, and can be called in script checks or whatnot.
Thresholds can sort of be set. You can use the success rate modifiers to create a recipe that has a 100% success rate, but requires level 3, and subtracts 5% (or whatever) per level under 3 you are. It's not quite what you were looking for, but should be serviceable.