Nothing happened until recently, when a bright, irregular lemon-yellow stain appeared under it.

Now I know that stain removal starts with identifying the source of the stain. In this case we don't have a clue. The towel was dry but could possibly have become wet in the past from water spilled nearby. The color is nothing like the reddish-yellow color of iron. The area is still waterproof (unsealed areas turn brown upon becoming wet; this area doesn't).

I have tried #40 hydrogen peroxide with ammonia (Windex) and also bleach (separately!). Perhaps there is no reason they should work if the area repels water, but anyway they didn't work.

Any suggestions appreciated.

Sorry I don't have any suggestions...don't have granite yet.
I hope some others will give you a solution :)

when you tried the solvents did you make a poultice?

if no heres how to remove a stain:

make a poultice of the solvent mixed with diatamaceous earth or baking soda. should be wet but not runny.

put poultice over stain area and cover the poultice with plastic wrap. Tape down the plastic on 3 sides. (this allows the poultice to dry much more slowly, usually a co uple of days)

repeat if necessary.

if the stain is oil based it helps to warm up the stone.