It's a very unfortunate legacy solution, mostly caused by the fact that both clean and not clean arrivals are mixing in the non-Schengen terminal (the Schengen terminal has a central security with fast track).

There are plans to change the entire terminal setup at PRG, which should also include central security for non-Schengen flights (which will then be handled at both T1 and T2) but it's gonna take a few years.