If proteins can traverse the sequence space over time, that means they don’t have to remain “near each other”. Also, that doesn’t mean that every single proteins evolved from one another. That is not what I am saying ether.
Sure, unless you want to define “motor” so broadly, such that you would call some protein complexes “motors”… which is likely what you were getting at with this… then I would say that SOME motors are designed. We can conclude that THOSE motors are designed, because we have the background knowledge. This isn’t the case for the other “motors” and we can’t conclude they are designed because they “look” designed.
Although, I wouldn’t call any biological system “motors” since such analogies poorly describe biological processes. Organisms are not machines.