You clearly do not comprehend the problem. Let's take the great apes and humans as an example. There is an oft-cited "statistic" that humans and great apes have almost identical genetic make-up. If you are talking about gross genetic content, that may well be example. the problem is the relative placement of specific genes within specific chromosomes. Even if you were to artificially equalize the number of chromosome pairs (humans have one less pair), humans and simians cannot reproduce because the chromosomes don't properly pair. This should immediately raise a red flag for the claim that humans and simians share a common evolutionary path. Not only would one have to account for an all but impossible case of identical extrachrmosomal or subchromosomal variation occurring in both a male and female within the same breeding population at the same time and just happening to mate, you would then have to account for the juggling of genes from one chromosome set to another (for which there is no known mechanism). So you wouldn't simply need to have these near-identical variants to occur in males and females in the same breeding population at the same time once, but once for the extrachromosomal or subchromosomal variation and once for each of the many remappings of genes into alternate chromosomes.
This isn't unlikely at all. Different numbers of chromosomes have been found in DNA extracted from Neanderthals. If Neanderthals -- which we know were a specific breeding community -- had that much variation, why couldn't others in the human family tree?
How do you know this? Seriously. It may or may not be the case. I just wasn't aware that the experiment had been done (and published). Please elaborate. Individuals and even species with different chromosome arrangements CAN reproduce. Not always, of course, but sometimes. It's not determined simply by how the chromosomes are split up.
Your whole point that a chromosome level mutation automatically means that the chromosomes can't properly pair and match up during mitosis and meiosis is simply wrong. Some chromosomal mutations, such as centric fusions, can change chromosome numbers without even reducing (let alone eliminating) fertility at least in the heterozygous state.
In fact does anybody know if the number of centromeres -- or the number of chromosome "arms" -- actually differs in humans and apes?
This doesn't stop horses and donkeys from reproducing.