The maintainers might answer specifically for recount3, but in general PCR (or any) duplication is not removed in RNA-seq (or targeted assays in general) without presence of UMIs in the library prep as duplication (especially for highly-expressed genes) is expected and removal would unacceptably reduce the dynamic range of count. There is no reputable RNA-seq pipeline that to my knowledge does that.

The test tube containing the PCR mix will be placed in the incubation chamber of the Thermo cycler, which in Vietnam is often called a PCR machine. The temperature inside the incubation chamber of the baldi's basics PCR machine will change periodically, thanks to which DNA replication can take place

This addresses multimappers though, not PCR duplicates created during PCR amplification of the library in the lab.