The scripts created in the bin directory suggest that properties other than logical file name, physical file name and target file group are indeed ignored. Eventually I solved this issue by adding a post-deployment script. To do this right click the database project and choose Add -> New item -> User scripts -> Post-Deployment Script. In this script you can modify the database anyway you want, in this case alter file's properties with:
ALTER DATABASE [$(DatabaseName)]
MODIFY FILE
(
NAME = [SqlFile1],
SIZE = 5000MB,
MAXSIZE = UNLIMITED,
FILEGROWTH = 50%
)