Oliver U. shared this idea
I do not see any artifacts in the #3 zoomed in (but try to disable GPU and compare, just in case), and Pathfinder leaves no edgelines cut for me. Here is the GIF when I subtract the top sector from the bottom one — nothing extra is generated like the #2.
Oliver U. commented
Störende Artefakte unter Pathfinder durch Transparents am Rand des Flächenausschnittes