As your previous post, now in v3.x there is two concepts: Catalog and Model. The catalog is your DB representation, so you can't have different scale/precision of that in your DB there. The Model is different, the model represents the entities you will use as objects in your code. The model may be different of your Catalog, for instance: different names, different mandatory fields (IsOptional), model-only relationships, value types, etc.
The Length precision scale follow db length precision scale Project setting should work indeed, but only if you do the change in the Model. If you do the change in your catalog explorer, LLBLGen thinks you actually want to change the DB, that's why LLBLGen will ask you to generate a schema update sql script.
I'm not sure where are you doing that change. However doing a Model entity field precision = 4 where the Catalog says precision=2 might cause SQL overflows errors. If LLBLGen is reseting the precision to 2 is for a reason, Are you sure your DB have all precision to 4?