I see what you mean, but the truth of that statement actually depends in part on how much background knowledge we include when considering the hypothesis of common descent.
In total ignorance of chromosome numbers from any species, common descent predicts nothing about the number, or changes in numbers of chromosomes, nor anything about how they would or even could change. Thus finding any particular number of chromosomes in some species is neither evidence for or against common descent if we know nothing about it.
It is only in the context of knowledge of differences among the numbers of chromosomes between related species, and additional information about the mechanism of inheritance (and I gather, also, evidence from similarities in chromosome bands between chromosomes from different species), that common descent entails that a fusion took place. Only when this background knowledge is included does a chromosomal fusion become evidence for common descent, beyond it’s absence merely constituting a potential falsification.
But that door swings both ways also. Differences in the number of chromosomes only becomes a potential falsification of common descent in the context of knowledge that implies either that there is no way for the number of chromosomes to change (because there is no mechanism for it), or that such changes would be overwhelmingly more likely to be strongly deleterious.
In the same way, differences in the relative proportions of transitions to transversions only becomes evidence for common descent in the context of knowledge of transition bias. Without this knowledge, common descent doesn’t predict these relative proportions. But once included, it essentially demands it, and thus becomes evidence for it.
One could go even further and say the same thing about trees and nesting hierarchies. To get a nesting hierarchy there has to be not only descent but also modification. Perfect inheritance even along splitting lines of descent, while that would result in genalogical trees would not yield any trees in the data, and thus common descent would not predict a nested hierarchy. It is only in the context of knowledge that descent includes change(however it might arise) that common descent entails a tree in the data.