I've never had to use different configurations for different games at least in ePSXe and the right plugins, but then again, I'm on Windows. I don't use Linux and I've seldom used PCSX for that matter, but judging by the screenshots there's definitely something wonky in the way the emulator/graphics plugin handles video scaling.
But yeah, video scaling should always be a proper multiple of the game own resolution, otherwise you end up with something close or worse than those screenshots.
p.s. What the hell is that blue rectable behind the game screen?