Asked my forum-shy friend for some feedback on this, here goes.
1. There’s no real benefit of using CSync on the RGB amp. It’s mainly there for SNES consoles that don’t have CSync to begin with and also if you have a Scart cable that has a straight through sync connection then there is no need to add a 470ohm resistor if you configure the jumper correctly on the RGB amp.
2. using the existing CSync circuit in the SNES will be fine although you won’t be any better off either as it is strongly advisable to make sure that you have a 470ohm resistor installed in your Scart cable if using the existing CSync circuit in the SNES anyway.
3. No, nothing different just don’t bother to wire CSync to the RGB amp and as you said leave R12 and C46 alone. Also don’t forget to disconnect the outgoing side of the S-RGB amp by removing R15, R16 and R17
The part that repeats R12 is supposed to say R11, R12 and C46.