Remember that the marks are not always completely correct. They are pre marked on the swing before it's all welded together so they can be up to one full mark out from each other. Have had that on previous bikes also.
There are lots of different ways to check alignment, from laser tools to planks of wood etc
I measure distance from the frame centre bolt to the axle bolt on each side (or I did, my new exhaust is in the way now)
If the wheel is already aligned you just need to be sure you move left and right the same number of marks each time you adjust the chain.