It's the same interface with the same colors as for example Border Guard and Miller which (to me) fall into the same category of effect. It is the same color for what you select from to topdeck with Artisan. It's the same color as when you decide what to top/bottomdeck with Sybil.
Yellow is simply the color of "make a selction now", context dependent on what happens. Red is trashing, green playing, orange Exiling, special cases of selection that happen offen enough to have their own color.
I can see that if you associate yellow with discarding, this interface is confusing. But unlike Advsisor or Envoy, you are primarily choosing what to "keep", that the other cards are discarded is just the "cleanup" of the abilty, they could have been put back, as e.g. Wandering Ministrel and Apothecary do.