To me this looks like an issue with someone accepting or creating artwork that needs a bleed off the sky/mountain, or larger border. And a plotter that's not dialed in or understood quite as well as it could be. I don't know how large the final product is, but I'd either have fabricated the bleed, or made the border 3-4 times as large, then we wouldn't be worrying about it.
I have no doubt the designer can align two simple shapes. I think they're being misunderstood and were just trying to convey that the final product would not appear aligned no matter how they set it up. And voila, it doesn't look great.
In my experience, circles and rectangles are going to show tolerance limits on cutters more obviously than more complex shapes. It's also easier for the eye to catch any alignment issues on symmetrical shapes with small borders.
If it's not already understood, I'd train yourself and/or the sales folks to not accept things that don't have an 1/8th inch bleed, and at least an 1/8th to 1/4" inch border/margin. Everything you create will look better as a result. No printer, plotter, cutter, is going to be perfect, so you'll always be beating your head against the wall otherwise.
I'd say the number one skill a designer/prepress person can have is just faking bleeds all day long and not raising a stink or even telling anyone.... Sad truths if you've ever been there. ;p