That is exactly the point.
Taking a theory (Systems Thinking), a mental model which has the primary goal of holistically identifying, describing, and understanding wholes and reducing it down to a set of methods/framework out of ease of use (the pragmatism) is exactly the wrong approach in my opinion.
Systems Thinking and all of its applications scenarios are based on epistemology. To turn it into a recipe is a wrongdoing. The whole notion is that one size does not fit all.
The operationalization of Systems Theory for a given case at hand is the responsibility and the transfer function of the operator whose approach this is. The process itself yields understanding and should not be abbreviated.
I practiced Design Thinking at IDEO for 10 years, and I can assure you it's not "one size fits all." And you can onboard an intern or a client CEO in days, without requiring them to internalize a very abstract system for decomposing problems.
So your argument is don't use an off the shelf tool that gets the job done, build your own tool every time which likely doesn't offer any advantage over the standard tool?
If you think using Design Thinking goes against Systems Thinking, I don't think you really get either.