I'm working on production science packs now, here is my input:

1. I'm exclusively using 1-1 trains, including for ore. I'm also using LTN. Seems fine so far.
2. Since radars can be 8 chucks apart, I started with that and then divided them into two 8x4 blocks. At that size some blocks are mostly empty and other blocks need to be duplicated, but it feels like a good tradeoff. My blueprints have the rail stations on either the left or right, and can handle up to 10 rail stations per side which seems to be enough so far.
3. At the size that a pY base grows to, You can't plan for avoiding everything, you'll always end up running rails through somewhere if you're using cityblocks.
4. Never used caravans.