Update: I found that just the following are suffient to enable RGB mode:

/var/hack/iicsetw 0x42h 0x02h 177
/var/hack/iicsetw 0x42h 0x29h 192

This doesn't seem to trigger the horizontal shift issue. However I am also now using LJ's fpa7114.o file from here. The picture quality is far better with no artifacts, and so are the colours, but not sure about whether they are optimal just yet.

I tried patching the fpa7114.o file, finding the relevant offset location from this thread, however I haven't quite found registers that survive a channel change as yet. I'm wondering if the fpa7114.0 module only gets read on boot up, and perhaps something else such as palmod is overwriting the values on channel change. More investigative work to do here!