See the emphasis on transparent substitutes in the article. This analysis is limited strictly to sets of instances that are fully hardware compatible, meaning AWS could resell one instance as another. There are way more savings to be had as a customer by leveraging instances that aren't transparent substitutes.
Which instances are not transparent substitutes, in your opinion? Keep in mind the defintion here is that Amazon could substitute the image transparently, e.g., by ignoring the additional resources in hypervisor, not that the instances are by default indistinguishable.
That being said, the substitute instances considered could be trivially accepted by any task running on the original instance, so long as it doesn't misbehave when given too many resources. In the case of vCPU, you can even hide extra vCPU cores, so a c6g.xlarge can be made effectively indistinguishable from a m6g.2xlarge by disabling the vCPUs at the hypervisor level.
