First, regarding resolution.
The RT2xPro will switch the HDMI output resolution according to PAL/NTSC.
Color Bars are always NTSC (480p), PAL consoles are (576p), NTSC consoles are 480p.
Regarding PAL color saturation;
PAL cables have additional 75ohm resistors in the cable, so a darker luma is expected and behaves like a CRT would, so the user adjusted for that in the old CRT.
In your case it seems that your TV over-saturates the HDMI input PAL signal, but not in Composite input, since it affect all your PAL consoles even PS2 which it should not (I have tested multiple PAL consoles).
Did you try to lower Saturation and bring Contrast up in your TV menu with PAL HDMI signal?