It’s the chance of getting the same tree as that inferred from another gene, or morphology, is extremely low yes. Presumably some designer would “fine tune” the gene sequence for their functions, not for the phylogenetic trees they produce. So since there are so many possible, functionally equivalent sequences even among the set that are similar, it is still extremely unlikely that fine-tuning towards function should end up yielding a tree that agrees with the tree from a different independent gene or the tree from morphology.
That means you would have to posit that the designer is deliberately picking the sequences that yield similar trees. But then the designer would be deliberately picking sequences that give the same evidence at that expected from common descent, so he’d be faking his data to give the deceptive appearance of having been produced by a process of common descent.
is extremly low, and thus it support common decent? is that your main point basically?
Yes, because common descent explains why the trees from different genes and from morphology are so highly similar. We expect this pattern from common descent, we don’t expect it from design. To expect it on design, we have to posit a deceptive designer using a really weird criterion for picking the functional sequences that he does.
It all gets even worse when we consider nonfunctional sequences. Pseudogenes, retroviral sequences, degraded transposons, introns, and many other types of junk-DNA. Why should these nonfunctional stretches of DNA also yield the same trees when they are under almost zero sequence constraints(besides merely not being deleterious)?