Personally I think it looks kind of cool/unique. But I'm of the opinion that having gear that inspires us is important, so if the looks bother you, I would find a way to remedy the situation one way or another (whether that's staining it, sending it back for another unit, or deciding you like how it looks). If it doesn't invite you to sit down and create music you won't get the most out of it.
Thank you for the thoughtful reply, and I do generally agree with what you're saying. To be clear, it wouldn't make any difference to me creatively if all the wood bits were made of warped particle board because I bought this amazing thing for its sound.
That said, I don't think it's unreasonable to expect appearance to match performance at this price. If I bought an expensive sports car that came with a fender painted in a different color than the rest of the car, it would have zero impact on the way I felt when driving the car, but I would certainly expect the issue to be corrected because I paid for function and form, not just function.
Honestly, now that I've had some time to think about it, the most likely outcome here is that I will just make my own custom end pieces for my Prophet. This actually sounds like a fun project, and it should add another layer of intimacy to our burgeoning relationship.
This is my Prophet. There are many like it, but this one is mine