How do we know that it wasn't made with a second centrosome, and imbedded telomeres, including a set backwards?
How do you know that shernren is really a human being? How do you know that shernren isn't really a supercomputer programmed with all the attributes, vocabulary, and attitudes of a human forumer, designed simply as another facet of the worldwide Matrix designed to keep humans in hypnosis while machines suck out their life-force for energy?
The whole problem is that you are trying to salvage the creation hypothesis by changing it into a "trickster hypothesis" (to use the ideas and illustrations of Elliott Sober). Your original hypothesis was:
H(Design) God, as a good designer, designed everything perfectly and did not use evolution.
When confronted with this observation:
A particular human chromosome looks like it is the result of two ape chromosomes merged, with no good design reason for it to look that way
and this hypothesis:
H(Evolution) Evolution can explain how a human chromosome looks like two ape chromosomes merged,
you are challenged to come up with a new hypothesis:
H (Design-trickster) God designed man, but did it in such a way as to make him look evolved.
You are right in that we cannot choose between your hypothesis and ours on the basis of evidence alone, because you have designed your hypothesis in such a way that it is
predictively equivalent to ours. In layman's terms, anything evolution can explain, the hypothesis that "God created to look evolved" also can "explain".
But firstly, this is no good reason to reject evolution, because by analogy it is possible to construct many other trickster hypotheses. For example, you are looking at a computer right now, right?
Observation: Something looking like a computer is in front of me.
H(Computer) There is a computer in front of me.
H(Alien) There is an alien in front of me who is using very powerful psychic powers to deceive me into seeing and interacting with something like a computer in front of me instead of it.
Just because
H(Alien) is predictively equivalent to
H(Computer) doesn't make the computer hypothesis any less convincing. We could construct similar "trickster hypotheses" for many other things we know to be true, but that wouldn't make them any less true or convincing. In the same way, just because your hypothesis is predictively equivalent doesn't diminish the validity of evolution, even if it somehow increases the validity of creationism.
Secondly, the trickster hypothesis introduces very different auxiliary observations about God into a Christian worldview. The original design hypothesis could actually have been broken into:
H(Design) - God designed everything
A(Perfect) - God wanted everything to be perfectly designed
while your hypothesis is now:
H(Design) - God designed everything
A(Trickster) - God wanted everything to look like it evolved.
We learn a lot about God's character from the idea that He wanted everything to look perfect. What would we learn about God's character if creation told us that He wanted everything to look like it evolved without any better reason?