1. NES and PC-engine do not output RGB natively. They need to be modded or use external adapter (PC-engine). You do not need to do individual settings, generic 4:3 mode looks perfectly fine out of the box (imho). Note that the linedoubling of 480i (relevant for PS2 especially) is not to everyones taste, passthrough may look better in that case.
2. The four Toshibas that have been reported have good compatibility for higher linemodes. This still doesn’t guarantee your particular model, but odds are favorable I’d say.
3. This totally depends on which 4k tv you had in mind and what you are comparing with.