You are definitely on to something here, and it's not the simple perfect hits vs good hits. Why would they do that though? Is it unintended? It seems like max skill sharded characters act like they have zero skill shards used while on autofarm. None of my characters that have no skill shards used on them play any different on auto though. Talk about weird bugs.
If they use a compiler of some sort, they should experiment with not using it for a few updates to see if it cuts down on the bugs. My experience with them is that they cause more issues than they do to help to save space.