notice how the cxa1645 has 24 pins but the 32x encoder has 32 pins...
Also the fact that the 32x encoder is wired completely different from how you would wire a cxa1645.
The rgb that comes out of the cxa1145 is not "bypassing" the cxa1145.
My genesis 3 consoles that use the built in cxa1645 have jailbars in the s-video picture. I've bypassed the cxa1145 in my model 1 with a cxa1645, even a cxa2075, and they all get the jailbars. The jailbars come from the vdp chip.