The second option looks a little better.

Aesthetically I like the look of the glass back splash meeting the flat surface of the stone. If installed properly the seal will be fine.

I agree I like the look of #2 the trick with the seal is a good install of clear silicone when all the tiling is finished.

Without a doubt have the tile come straight down to the countertop. It is too busy of a look with a standard 4" backsplash (3/4" or 1-1/4" thickness) then a glass backsplash (3/8" thickness). The seal will be fine as long as your tile setter grouts it properly and then adds a clear coat of silicone afterwards.