Purpleheart doesn't get finished. It's used raw, like rosewood and ebony. If you order a finish with your neck, only the maple (or mahogany) areas will be sprayed, and the purpleheart will be left alone.
If, for some bizarre reason, you did paint purpleheart with clear coat, it would not affect the colour. Clear poly takes a few years to yellow, and when it does it's very gradual. Even at maximum yellowing, purple is one of the strongest colours to not look any different (others being red, orange, green, and of course, black). It's only really blue, pink, and white finishes which show yellowing particularly strongly.
But also note that the way Warmoth photographs purpleheart makes it look a little different than it does in reality. (Same goes for all of Warmoth's photography, really; they really gotta get someone who knows what they're doing.) Purpleheart, in person, is a fair bit darker than it ever looks on their site. It's about as dark as the lightest rosewood, but obviously a different hue. It's also a fraction redder than it is on the site. So if the particular colour is important to you, bear that in mind.