Is it permissible for a Jordanian engineer to receive a salary from the Engineers Association for six months, along with a certificate of experience, in exchange for training at a company that will secure him a job later, knowing that the trainee finds the job opportunity himself?

So long as the syndicate knows that you are receiving a salary from the company where you are training, and it still grants you a salary, then there is no harm upon you in benefiting from the syndicate's salary. And there is absolutely no harm upon you in benefiting from the certificate.