I wrote a small nanopass-style compiler (with many small passes) and had the same experience: lots of redundancy, and hard to debug because it wasn't clear how the passes interacted.

Admittedly, this framework has extensive metaprogramming (it's a Racket DSL), so it probably has much less redundancy, but is probably even harder to debug.

To an extent, it's impossible to implement nanopass in a way that's neither redundant nor confusing, without a projectional editor. Because either each pass's AST is fully redefined, which adds redundancy, or most pass's ASTs are defined in many places, which adds confusion. But my wild speculation is that one day projectional editors will gain popularity, and someone will make a compiler where one observe and debug individual passes.