Yes. As I stated in a past thread, I'm taking supernatural designers off the table.
This limits you to a universe with a finite history. This means that at some point in the past your designer had to come about by natural means. I don't think it is much of a stretch to suggest that this first designer would be as complex as we are, biologically speaking, and I would expect that this complexity would include irreducibly complex systems as well.
For all intents and purposes, it appears to me that we are those First Designers.
For if life was designed by engineers with a radically different kind of intelligence — a form of intelligence entirely foreign to that of the human species — it would be a hopeless task to find traces of engineering in cellular life.
I completely disagree. Humans are not limited to a nested hierarchy when they make designs, and neither would another intelligence. I would expect that their vehicles and technology would also not fall into a nested hierarchy just as our technology does not. Only evolution consistently produces a nested hierarchy (for species that do not participate in horizontal genetic transfer). At best, you would have an alien race dropping off LUCA 4 billion years ago and never touching life from that point onwards.