The stored procedure calls create new connections and are not using the timeout values from the database. This was fixed in a pull request into rhallman/EntityFrameworkExtras
command.CommandText = query;
command.CommandType = CommandType.Text;
int? commandTimeout = database.GetCommandTimeout();
if (commandTimeout.HasValue)
{
command.CommandTimeout = commandTimeout.Value;
}
command.Parameters.AddRange(parameters);
database.OpenConnection();