Is the percentage taken by an employee overseeing publications from the printing press he deals with, without the knowledge of his employer, considered embezzlement and theft, even though all documents and invoices are sound and legal?

The ruling on the percentage you take from the printing press owner is the ruling on gifts to workers, and it is not permissible except with the permission of the authorized government official. This is because it has been forbidden in authentic hadiths. In the Sahihayn, Abu Humayd al-Sa'idi reported that the Prophet (peace be upon him) said: "What is wrong with a worker whom I send, who then says: 'This is for you, and this was gifted to me'? Why did he not stay in his father's house or his mother's house to see if he would be gifted anything or not!" Therefore, even if this percentage is not embezzlement or theft, it is forbidden unless approved by the official.