Yes, thanks for the save file!
It makes sense that the lag would happen irrespective of any entities changing or of whether they're vanilla entities. The event data for a blueprint being placed doesn't contain information about entities; instead, to find any potentially affected entities, the code needs to search the full area over which the blueprint was placed. It also indexes these entities against their respective blueprint entities by position. So the only way for the mod code to know if an entity it cares about was affected is to go through that relatively expensive search process.
I expect this will be basically unfixable. There might be some possible optimizations, but a bigger blueprint is probably all it would take to negate any improvements. And it can even happen in vanilla, e.g. when placing those crazy overlapping rail blueprints (assuming that trick still works in 2.0).