@jezerinac
Yes, the methods to set fonts in usable fonts collection of API are thread specific and you need to initialize them each time a single thread is started execution. However, we have logged an investigation ticket as PDFJAVA-38332 in our issue tracking system to further investigate the feasibility of your requirements. As soon as we have some updates regarding ticket resolution, we will share with you.
Furthermore, it would also be helpful if you can please share a sample console application demonstrating the actual scenario you are experiencing. It would help us during investigation process.