This I can partially answer-- The Y/I/Q stuff is for NTSC simulation and had been described as being used with MESS consoles and computers.
While I cannot say with 100% certainty on the other, I'm pretty sure that the tunable scanlines are there to allow you to tweak based on output resolution and prescaling to get the "perfect" image output you want.
I'm betting this is something you'll need to tweak on a per-game-resolution basis as well.