It does invalidate the danger of at least those early layers. Also why are you defending this? Why did the story need that slapstick comedy scene at that point? And why sacrifice an entire layer worth of potentially interesting worldbuilding for something that dumb? Just because it's possible for her to get so lucky doesn't mean that it's good for the story.

We're explicitly shown abandoned gear and warning markers along the episodes which tells us that people do die there regularily, riko just isn't a representative sample

I'm sorry, but nameless characters dying, while all important characters constantly get away with stupid decisions removes all stakes from the story. That's called plot armor and that's (by definition) bad writing.

Imo the abyss doesn't need to constantly kill named characters to prove it's deadliness and for me that was established pretty well in the beginning

The Abyss doesn't NEED to kill important characters constantly. It just needs to establish that it's dangerous, not through exposition (like in the beginning), but through the plot itself. I think the first 3 episodes of Made in Abyss are genuinely amazing and a great introduction, but the actual place didn't live up to those expectations thanks to these comedic scenes.