You are viewing this issue in quite the binary way, as if all genes must be either ORFANs or homologous, leaving evolutionary biologists on the horns of a dilemma. This is quite contrary to the evidence biologists have published, and reflects a grave misunderstanding of how biologists think about this issue. You have also missed important advances in the articles you cited. All in all, you have not portrayed evolutionary theory or evidence accurately.
A tangent: I am not a biologist, but I have been reading mainstream biologists and ID biologists for about 20 years. I typically ask biologists such as @glipsnort to correct me if I have misunderstood something, and have learned much from the corrections they have given me. Given your background in the biological literature, I would heartily recommend that you follow a similar practice.
Back from the tangent. Roughly 90% of genes are homologous across species and 10% are ORFans, although this ratio can vary. The homologous genes are not sequence-identical; in fact, they almost invariably exhibit a pattern of nested hierarchy. Moreover, those nested hierarchies are almost invariably aligned with nested hierarchies based on other factors such as ERVs, amino acids, biological characters, and fossil characters. The existence of the nested hierarchies and their consilience provide powerful evidence of common descent. So biologists are not just starting with an assumption; common descent flows from the strong mathematical evidence provided by nested hierarchy studies.
But evolutionary theory has not until very recently shed much light on the other 10%, the ORFans, as Anne Gauger noted in 2019. Of course, the incompleteness of a theory does not imply that what a theory has explained and predicted is necessarily wrong. To take an example from another scientific field, the inability so far of astrophysicists to fully explain the nature of dark matter does not imply that it does not exist, and most certainly does not imply that the Big Bang did not occur.
But significant progress on ORFans has been made quite recently. One of the findings was in an article you cited, but somehow you missed it:
Our results presented the first systematic evidence on the evolution of orphan genes and de novo origin of genes in nematodes and their impacts on the functional and phenotypic evolution, and thus could shed new light on our appreciation of the importance of these new genes.
In bacteria, a class of ORFans seems to play a role in pathogenicity, as explained in another passage you missed in a different cited article:
All of these findings suggest the greater importance of PS-ORFans for bacterial pathogenicity.
The contribution of the 2021 article I cited was its demonstration of the likelihood (indeed, the inevitability) of the evolution of ORFan genes from non-coding sequences. This does not contradict anything about homologous genes; it is simply another evolutionary mechanism that biologists are understanding more and more.
The reason I cited that article was that it shows that your mathematical analysis of genetic evolution is indeed based on the Texas Sharpshooter Fallacy.
You do not seem to want to learn from the community of biologists, Thomas. Here’s an analogy: If you are determined to take ivermectin as COVID prophylaxis and you’re willing to look hard enough, you can find a doctor to prescribe it for you. (I would strongly discourage it, because the best reviews based on random controlled studies show that ivermectin has no positive effect on COVID prevention or treatment.) Similarly, if you look hard enough, you can find a biologist who rejects the consensus of the other 99.9% of biologists.
Here’s a sincere question for you, though: Have you considered learning what the other 99.9% really say? So far, you have manifested no understanding of either the theory or the evidence of evolutionary biology. I do not say this as a criticism of your intellect or sincerity, Thomas. To use yet another analogy, I know nothing about click languages and couldn’t understand a single statement by a speaker of such a language, but I do not consequently feel stupid. However, it would be quite infelicitous of me to assert that an African who was clicking or whistling was not communicating complex thoughts simply because speakers of the languages I happen to know do not use clicks or whistles to communicate complex thoughts.
Are you interested in spending a few months to acquire a reasonable background in evolutionary biology? If so, folks around here (including me) would be happy to suggest some resources.