Dependencies detection broken ?

Addressables uses AssetsDatabase.GetDependencies to determine the dependencies (at least on the Analyze rule) but the result from AssetsDatabase.GetDependencies is not reliable.
It gives different result compared to select the scene in the project, right click -> Select Dependencies.

I have spent hours cleaning a scene to find out that the main issue is caused by adding any script. When a script is added , all the .cs files are included - seems normal to this points but it also some prefabs which then cascade into including a load of assets.

It would help if we could get a dependency tree as on large project this is nearly impossible to track down.