No, that logic doesn't apply. The examples you listed don't fit the 3 or 4FNC rocket type. The major difference between a 3D printed 3FNC and a conventionally built one is the method of construction. They are the same design when it comes to loading and stability. This is not true for the examples you gave.The same logic applies to flying pyramids, spools, and other oddroc designs, but I have heard zero complaints from people that those are specifically disallowed for cert flights.
I really don't think this restriction is that unreasonable. Once you're certified, you can do whatever you want, but L3 cert projects need to be easily evaluated by TAP members.
I agree with your point that TAPs need to be able to assess cert projects. But if TAPs are certifying 3D printed fin cans on L1 & L2 projects I don't think that L3 requires any additional special considerations for evaluation of the fin can. You're still evaluating the same basic thing, will the design presented withstand flight loads.
I still maintain that the certification process is demonstrating that the applicant can build and fly a 3 or 4FNC type (clarified because of the above point) amateur model rocket safely. The method of construction doesn't change this.