If you get a flicker that looks like a vertical shimmering, that’s because it’s an interlaced signal. This is, unfortunately, the norm for PS2 software.
The RT2X/Pro/SCART are all [relatively] simple line-doublers, so they can’t perform good deinterlacing–the most they can do is duplicate lines (or insert black lines when scanlines are turned on? I don’t have hands-on experience with these devices) to fill in the missing fields every frame in order to bring the video output from 480i/576i up to 480p/576p.
When you put these devices in passthrough mode, it leaves it up to a downstream processor or the display to perform deinterlacing. If that happens to be your display, and your display is in game mode, it wouldn’t surprise me if your display is just doing something similar to the RT2X Pro. In my case, my Samsung LCD looks like it’s filling in black instead of trying to do a bob deinterlace. If you want a good deinterlace, you’ll need to disable game mode on your display and take the tradeoff of added input lag.