1. The only difference between 3.5mm outputs and RCAs is that the 3.5mm have shared ground. Yes, you may get a slightly better sound through straight RCAs, but the difference is minimal at best.
2. I'm confused as to what you're saying here. Windows bootscreens are basically limited to certain colors (indexed) and only a certain number of them. That's just by design. In windows you can have as many colors as you want (16.7 million). What exactly are you asking? What you see depends on the software you have.
3. Yes. Centrafuse has a program called PhoneControl built in that does exactly that.