Definitely, the quiet and smooth changed with the chainline. It was 1mm off with the Shimano. You could barely tell but you could see the chain come onto the chainring at a very slight angle.
And yes, the Sugino BB lets the cranks sit in deeper. They're pretty close to the BB shell, with no odd gaps - whereas the Shimano showed quite a bit of gap. This of course has to do with the BB cup and cone sticking outwards but it also feels like it went on snugger. All of this is "feel" rather than actual science like you folks have been debating but sometimes, "feel" feels right.