I whole heartily agree with everything you say here. That said, it is difficult to judge at this stage whether DB actually has all the mechanisms necessary for eventually evolving something interesting/complex and we just need to run larger and longer sims (perhaps larger and longer than is possible with today's hardware and human lifetimes) or whether we are yet missing some critical mechanism without which nothing of merit will ever emerge no matter how long we wait.
As you say, it's not just the organisms themselves which are the product of billions of years of evolution but the genetic mechanisms they and evolution use and rely upon. Everything from DNA itself to chromosones, to gene structure to the copying machinery and the mutation patterns, types and probabilities that go with it evolved to and were selected for evolvability. The thing about DB is that a lot of this evolution machinery is hard coded in the simulator and thus not subject to selection. We can't evolve the right mutation/copying/gene structure machinery as nature did (or perhaps we can, but have yet to try). We have to hand code it and it has to be right or nothing of merit will ever emerge.
While it may be beyond our current patience and capabilites to evolve something truly meritious, I do think it within our capabilites to recognize when we have hit upon the necessary mechanisms and to know that something interesting can and would eventually emerge. It's just my opinion and intuition at this stage, but I think we are still missing some of those critical mechanisms (cheif amoung them, BP sequence relative mutation probabilites exposed to selection) and I hope that once we have them, we will notice the difference in the organisms we can evolve in reasonable time frames.