No, they don't have to line up.

Consider what you are planning on storing in them, though, and how often you need to access. Standard upper cabinets over washers/dryers tend not to be accesible beyond the bottom shelf for average-sized people. I basically didn't use the upper shelves in the cabinets in my last house - the cabinets themselves were too shallow for what I wanted to store there (towels) so were basically useless. In my current house, I'm planning on using refrigerator uppers above my machines for storing rarely-used items with a hanging rod for drying underneath, and just putting one upper cabinet over my sink.

I don't have the pic anymore of what I'm planning but you can see it in this post. https://www.houzz.com/discussions/6482386/laundry-room-paint-cabinet-color-help

I would say No, they don't have to line up. Just be careful with their height at bottoms. I have found with my own, I can't quite fit a front loading washer on a pedestal, under cabinet lighting built in (which is silly, I'm washing clothes not performing surgery) with those built ins above. 1955 lovely all tile laundry room but not made for today's larger appliances. Front loading and its a deep low reach for me if machine sitting directly on the floor. Although I do have a mechanical reach. I keep cleaning cloths, clean rags, those products used only occasionally in the cupboard above along with some specialty products used elsewhere in the house and outdoors. Step stool in the utility closet opposite wall and I do have one of the hand-held mechanical reaches for lighter objects stored up there. So far I've had to stay with a top loading washing machine -it's that or call in a carpenter!

I have a top load. There is an office here as well plus all the cat food supplies along with laundry detergents. So yes, I need some storage. Maybe I will do open shelves above the sink and then two cabinets then a rod to hang shirts or no dryer apparel.