In a word - yes. The Watco involves some pigment, and that will collect in the endgrain and give the piece a contrast the natural wood will never have. If you're doing a Pho, you might like it, but if you're looking for natural, let it mellow in. Else expect garishly dark endgrain and light face grain even with a mild stain like the Watco. If you burnish the wood you can get things a bit more equal.
The chemistry that darkens the wood can be helped by high energy light. It can be retarded by kinl-drying which involves leaching initially and then usually a final steam to relax case-hardening. KD cherry will want more time.