1.1. The screen resolution stencils for iPhone and iPad are already the correct size for devices with Retina displays. The on-screen dimensions in points are the same on devices both with and without Retina displays. FileMaker scales the graphics up or down for each pixel density as appropriate.
1.2. FileMaker Go for iPhone has not been updated yet to accomodate the larger iPhone 5 screen dimensions. It runs letterboxed. So having a layout stencil tailored for that screen dimension might be jumping the gun a bit. If you wanted to go ahead and start designing for iPhone 5 dimensions in anticipation of a version of FileMaker Go that isn't letterboxed, you could make a custom stencil size for the appropriate dimensions: 320x473 for portrait orientation, and 568x255 for landscape, if my calculations are correct and FileMaker doesn't change the size of its chrome in Go.
2. I agree. Saving custom stencils would be nice.
3. Personally, I think it will be a best practice to continue designing layouts to work well in the smaller iPhone screen, with objects that intelligently auto-resize for the larger screen. I will be updating my scripts for previewing iDevice window sizes on the desktop to include iPhone 5 dimensions, though.
FileMaker Go 12 for iPhone has now been updated to use the screen dimensions of the iPhone 5 and the latest iteration of the iPod Touch.