Hmmm....I have used the serial console of the early boot process before to debug a bad dd-wrt (openwrt fork) image on a router. I suspect that this "feature" is enabled by default in the openwrt build process since this is a relatively good way to unbrick a board with a corrupt flash image.
A bootlog for linino is at: linino/bootlog at master · arduino/linino · GitHub. There are several opportunities that echoing the console is not a good idea!
Took a bit of digging, but it appears the only way to stop the "terminal chatter" early in the boot process is to rebuild the kernel to disable "Early printk". Not something that most folks (including me) will be excited about for many reasons. Seems like the best workaround is exactly what scrot and wayoda are doing: find a way to make sure the 32u4 does not respond to this "terminal chatter".