First and most obvious question: are you sure that your PAL Roms aren't simply being sped up and running at 60Hz?
The refresh misalignment from a 50Hz game on a 60Hz display isn't all that noticeable, and certainly not in games that run at frame rates lower than the console's host refresh rate. Chaos Engine and God's definitely fall under that category as games that run at 25fps/30fps.
If you have games running at a smooth 50fps on 60fps display and there's a lot of movement along one axis (horizontal or vertical scrolling), the judder will be somewhat more apparent.
RetroPie emulators can be configured from the emulator launch menu to support a 50Hz refresh rate if your display supports it. I've found that this does make a slight but worthwhile difference, especially with C64 and console games.