It looks like I managed to create a working solution, but I also have several questions :-)
Regarding the solution, it was not too complicated. I modified ClosureWriter and StaticTypesClosureWriter to annotate generated call methods with @Generated. Regarding questions. Modification started to work on an external project only after I locally installed a non-snapshot version of Groovy. I didn't manage to make it work with the snapshot version. It can be related to Gradle scripts that the external project uses, but I wonder if it has something with Groovy itself or its install/release process? As another puzzle, I noticed that some generated closure classes already have "doCall" method annotated with @Generated. I wasn't able to find who is creating that method. Although it doesn't conflict with modifications in any way, I will like to know who created it? Tnx
