Else all the Amigas blitting routines and so forth would have wrong clip limits, wrong overscan limits, etc. Nothing will work right.
Setting the refresh rate doesn't change how much chip ram has been allocated for the screen, so blitting would never be affected.
I'm pretty sure that it just leaves a blank area or clips the screen, depending on whether you're going from NTSC to PAL or PAL to NTSC.
Most games never look at execbase, they just open the screen they want (and usually with custom copper lists). Running a PAL game on an NTSC Amiga just crops the bottom off.