I think if the project is in(file(".")), it is the root project and default source position would be src/main/scala/main.scala. Unless the project included multiple modules, I see no need to place it in the additional directory.
As suggested by @Jasper-M, if the sources should be located in core directory, a natural thing would be to use just project or project.in(file("core")), which is the same thing if the project variable is called core, and then the default source position would then be core/src/main/scala/main.scala.
Overriding scalaSource is always possible, or you can manipulate unmanagedSourceDirectories , e.g. in my project I use this to add additional source folder: