There is a difference between those examples and a whole 5 minute stretch of time where we’re supposed to feel nervous for the droids because they’re in a dangerous wasteland.
The Jedi are mentioned quite a bit in the Original Trilogy, and they come across as mysterious because you have no real sense of how their Order was structured, what their rules were, or what their temple looked like. Watching those films, you are left with a sense of mystery surrounding the Jedi simply because you know so little about them. If you watch the Prequels first, they take that mystery away.
The same applies to the Empire. It is not mysterious in the sense that we do not know what it is, but rather in the sense that we do not know how it came to be. How was the Empire established? Who is this Emperor we see in the films? What connection did he have to the Old Republic? These are all unanswered questions when watching the Original Trilogy, and the Prequels take away that mystery by giving us all the answers upfront.
So, if we were to follow your logic and remove everything in the Prequels that diminishes the sense of mystery in the Original Trilogy, there would not be much of the Prequels left at all.
As for Tatooine, the Prequels do not ruin it. They only show a very small part of the planet, just like the Original Trilogy does. The Prequels never take us deep into the desert, nor do they explore its dangers. The story stays within a relatively civilized area where you have a clear idea of what to expect — exactly like in A New Hope. When the droids wander into the desert in A New Hope, the tension remains, even if you have seen the Prequels, because the desert is still an unknown. The Prequels only show the parts of Tatooine that are full of people, places where there are no real surprises. The desert, on the other hand, remains an unpredictable and dangerous place, no matter how much you have already seen in the Prequels.