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Well yeah, structure based design WOULD be a limiting factor- in an environment where structures are hard to come by. In a world with alphafold, that is no longer the case. Moreover alphafold can be run again- you can pop a small molecule in and refold the protein around it. 20 years ago, during my PhD, we used to use sybyl and autodock to do the same thing- frankly, those software tools were utter junk. Traditional drug design operates on the level of a blind man with a cane; we'd take a lead compound and add moieties to influence binding, essentially feeling our way along the binding pocket. With structure based design, we can now see.
The fact that it hasnt been a big part of drug design formerly isnt relevant to how new drugs will be disovered in the future. I am enormously doubtful that this authors view will hold, structure based design can only increase in significance