The author's overall point is fine (specifically, that one should consider developer cut-and-paste behavior as an indicator of unnecessary complexity in a tool). However, when discussing the designer's perspective, I think the author should have taken a broader view of complexity.
Much of the complexity in Makefiles stems from their generality; essentially, the set of problems to which a Makefile can be a solution. Substantively reducing this complexity necessarily means eliminating some of those use cases. In the case of make, this is clearly possible. Make as a Unix tool has been around for a looong time, and one can look at the early versions for an idea of how simple it could be.
But the rub is, simplifying make doesn't necessarily reduce complexity. Once armed with a simpler, but more limited make, developers are now tasked not only with knowing the easier Makefile syntax, but also knowing when make isn't an appropriate solution, and when and how to use whatever tool exists to fill the gap. Compounding this is the fact documentation and shared knowledge regarding which tool is appropriate for which problem is much harder to come by than documentation for the tool itself. This can easily lead to the tool choice equivalent of developer cut-and-paste behavior: "so-and-so uses build tool X so I must use it too", "if your doing (general description of problem) the only build tool you ever need is Y", "I used Z before, so I'm just going to make it work again".
Essentially you can think of make as one "verb" in a sprawling and uncoordinated domain-specific language that targets building things. Developers need some level of proficiency across this language to succeed at their work. But trading complexity that must be mastered in one tool for complexity that must be mastered across tools can very easily increase overall complexity and promote its own kind of "Makefile Effect", just at a different level.
EDIT: Some might prefer the term "Cargo Culting" rather than "Makefile Effect" here. I suggest they are the same behavior just in different contexts.