Hello there, comrades! I have a question.

If a specialization has a skill in its "bonus skills" which already is in main career skill list (for example, bounty hunter: assassin - this choice has Ranged (Heavy) both in main career and bonus skills), does it mean that one can get two free levels in it on character creation?

Yes, it states in the CRB that the PCs can train any skill they want to, but they require the XP and it cannot exceed rank 2 at character creation (Corellian Humans can train piloting to rank 3, but that's a special case.) The Technician explains this well, go to the description for the Mechanic (CRB pg 87), and it states in brackets that a Mechanic may start with 2 free ranks in Mechanics.

Thanks, comrade! Now that's clear.