The Doomsday Machine is a fairly generic engine of destruction which could be used as a backdrop for just about anything.
That's my thought as well. How much time do we see the Whale Probe on screen? Maybe 2 minutes? It's not the focus of the story. It's just a catalist of the story. And it's not some guy wanting revenge. Please anything but a guy wanting revenge.
Except we've already had two Trek movies about gigantic planet-destroying alien objects. And you just know they'd insist on putting Earth in danger this time.
In the original episode it was headed to Rigel. Rigel could be an Earth-like stand in without having to go to Earth.