I want to raise a few issues about papyrus and persistence.

Firstly there is a mod out there that the author has come under a bit of flack being accused of causing save bloat and breaking parts of their game - these may or may not be valid claims but the claims are being made that the mod leaves persistence on certain vanilla objects. Now I know how these scripts are applied to the objects via reference aliases, I don't know what the scripts have in them, the .psc files are not included. So is it possible that assigning scripts via reference aliases can induced persistence?

Secondly I have been chasing down some script problems with my modding partner and trawling through his papyrus logs I find these logs:-

 [03/25/2013 - 05:10:23AM] warning: Function AJHWaterLevelCycle.DownCycle.onBeginState in stack frame 3462 in stack 1939078 differs from the in-game resource files - using version from save

Now it strikes me that if the debug log can detect that a function differs from the save, why the bloody hell does the game choose to use the save version instead of the resource version? Is this a recipe for persistence problems and could a fix for some of these script persistence problem be solved by simply choosing the resource and not the save version?