Is it permissible for me to receive a private financial compensation for some of the transactions I perform at my job, without the knowledge of my employer, especially since I exert special effort in them and these transactions are discretionary?

It is permissible for you to request a salary increase, or a reduction in working hours, or an adjustment in the manner of work, by agreement with the owner of the bookstore. However, taking bookstore transactions for your personal gain without the owner's knowledge is not permissible. This is consuming wealth unjustly and a betrayal of trust, as Allah Almighty says: "O you who have believed, do not betray Allah and the Messenger or betray your trusts while you know [the consequence]," and the Prophet, peace and blessings be upon him, said: "Render back the trusts to those who entrusted you, and do not betray him who betrays you."