How can you build something that's interfertile with humans but can breathe in a vacuum?
Thornir's explaination is quite reasonable.
(Assuming the Boomer on Caprica isn't lying) How can you build something that's interfertile with humans but not with others of its own kind?
I think the assumption that might be off the mark is that they
want the copies to be intrafertile. I don't think that's the case. I think the cylon's religious/metaphysical beliefs are leading their 'experiment' - the idea of 'merging with their makers' in a very literal sense might be driving their efforts. Think of it as the religious stem-cell arguments in reverse
The basic problem is that something indistinguishable from a human by the tests Baltar came up with before his 'Cylon detector' can't be anything but pretty much human. [...] The technobabble around Baltar's Cylon detector is loony. If the human-looking Cylons are pretty much geneticly engineered humans (and if they're interfertile with humans, they have to be), then there may be telltale genetic markers that indicate Cylon bioengineering, but there's not going to be anything unusually about the underlying molecular structure.
My take on this is the cylons have pushed the limits on what 'genetically engineered' means. When we do it today, we're only working with existing information in a particular genome, manipulating existing characteristics to express themselves (or not), or, in some cases, simply splicing characteristics from another source to existing genes (like bioluminessence.)
We cannot, however, add totally new genes or genetic material designed from scratch. I think the cylons can, either by replacing the 'junk' DNA the human genome is full of, or by making the DNA strands of genes much more densely packed. This would have a different molecular structure. However, through a conventional microscope it could be made to still appear contained in the standard number of human chromosomes. Only rigorous genetic profiling (which is all the 'cylon detector' appears to be) would reveal the differences.
Think of it this way: in the computer world, you can have hardware system A which can run software which allows it to function as if the hardware system B. B is a virtual machine, by which A can now run software programs designed for B. So the cylon copies are running a human 'virtual machine' on top of their genome, which gives all the outward appearances of a human (from blood to interfertility with real humans.) The base machine (genome), however, contains all the 'extra-human' abilities - superior strength, 'uploading' of their consciousness to other copies at death, glowing spinal columns during sex...
However, should the cylon models intrabreed, it would be like system A trying to run another copy of system A, but through system B. Possible, but usually system B is less complex than A, so it is not capable of running a copy of A. A, however, is much more likely to be able to run another copy of B (a hybrid baby.) This is probably the approach the cylons are taking.
It likely takes a great deal of effort to design these base genomes plus the human gene expressions they are emulating, thus the limited number of models we see... The human genome being emulated might have to be very specific, also, and need to come from an actual human sample. This might be another reason behind the 'farms'. I also think Starbuck may be one of those with suitable characteristics, and we may be seeing a few copies of her as 'Model 13' (the model for Kobol?)
If you want to create a human-Cylon hybrid, and you've got highly advanced biotech, can't you just use human sperm or ova from one of the millions of dead people around instead of creating an elaborate set-up?
Again, I think the Cylons are letting the tenets of their belief system guide their efforts, and the more direct approach you suggest may not satisfy the metaphysical goal behind it all. (Doesn't matter if the naturally conceived hybrids are actually embued with a 'soul'; what matters is if the cylons believe they are.) They could do what you're suggesting, they just don't want to.
We don't know any of the limitations or failures of the process, yet. I'm willing to bet the human model cylons have lots of flaws and drawbacks...we just haven't seen them blatantly laid out, as of yet. For that matter, we don't know exactly how they're trying to reproduce....there may be restrictions based on holy doctrine which are limiting their approach.
