Second of all: The settling for ignorance might not last long. I will argue that "goddidit" would actually NOT be an acceptable dismissal. "How did God do it?" would become the main question.
"By magic". Thus: end of story.
An extended answer: The question isn't even close to being as meaningful as questions based around "How did this happen naturally?", as he might as well have used magic. God may have used the movement of continents, salinity clines, and sexual selection to differentiate two species of sea slugs, or he might just have used magic, and made the world look like all those factors were involved. Finding out which it is (was) is a pointless endeavour.
I don't see a serious downside. Evolution wouldn't crumble; designer or not, it's clear that this is how most of the diversity we see today arose.
Or: it was deliberately made to look that way, and there's immediately obvious way to tell which scenario is correct in a given case.
To give a more detailed example, I will use a paper I wrote a while ago. It treated speciation in the oligochaete
Lumbriculus variegatus. This species occurs in sexual and asexual populations, and the asexual populations are commonly found to be polyploid. Or, rather, populations are usually found to be polyploid and to reproduce asexually be fragmentation and subsequent regeneration. Even sexually mature individuals can do this regeneration, and that, as such, is not a sign of being polyploid or obligately asexual.
Christensen (1980) found that in tetraploid (4 sets of each chromosome (1)) populations, the production of sperm was impaired, and this, he extrapolated, might mean that individuals of higher ploidy-level may have even more defective sperm (though this was never specifically studied). Even the asexually reproducing individuals do develop their sexual organs, usually in the spring, though, but these -- as excellently shown by Mrazek (1907) -- are usually very aberrant, either lacking vital parts (2), having them distorted, or having them displaced (3).
For sexually reproducing individuals, this would be catastrophic, as they would be unable to reproduce, but for asexually reproducing ones, it is no problem, and might even be a sign of it. Free from the need for working genitals, there is no selection pressure on the genes that code for them, and thus any and all mutations that aren't harmful to the rest of the individual might conceivably remain in the population for an extended amount of time. They still get expressed, and give rise to these strange genitals, but that has no influence on the continued evolution of the population.
So far, the hypothesis holds.
Lumbriculus with abnormal sexual organs are likely to be evidence of an asexually reproducing population (4), which should evolve as do asexual populations of other organisms. This commonly means a transition from diploidy to higher ploidy, with all what that entails. The pattern, across the Metazoa, is quite clear, though exceptions do exist, mainly depending on what mode of asexual reproduction is employed.
However, if we need to introduce the "the pattern may or may not also be the work of a capricious god, and have absolutely nothing to do with the evolutionary history of the population", then what is the point in finding the pattern in the first place? And: can we trust that the pattern has anything to do with reality? If we find that there is an intelligent designer, but cannot ask him questions and get answers that we can somehow know is truthful, then the pattern we find may have nothing at all to do with the actual conditions these worms are living under. It may just be that God thinks that 11-ploid cells are prettier, and thus he changes them all into that, regardless of the evolutionary history of the population.
This, in various modified forms, would be applicable to all fields of biology. We see a pattern of extinctions of flightless rails and other island endemics when Europeans start to explore the world and bring dogs, pigs, cats and rats -- all potentially natural predators of rails and/or their eggs. Is this correlated, or did God just wake up one morning and decide that he didn't really like flightless rails, and then he got rid of them, and would have done so even if Europeans had never left Europe?
The moment we find Wowbagger's evidence, whatever it may be, biology transforms from a science into a guessing game. This is, primarily, because the strings that connect theory with reality would be severed. All papers that have anything to do with evolution would have to have the disclaimer "This paper represents what things would be like if here had been no intelligent designer, and are thus not necessarily reflective of the actual conditions of the present world". I think it is somewhat naïve to think that this would not make evolution crumble or, at least, become a somewhat pointless thought exercise.
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(1) Christensen found individuals with 11-ploid cells, which means 11 copied of each chromosome. He also reported, and I have seen this myself, individuals which had even more chromosomes, but after 180, it's too crowded to be able to count them... No upper limit is thus known.
(2) Apart from organs that produce eggs and sperms, there are also generally transportation tubes, receptive chambers, chambers for storing received sperm, glands for deposition and so on -- any or all of which may be missing.
(3) This may not seem so strange for a mammal like us, as we would survive and be able to reproduce, supposing we found a willing partner, even if our penises and vaginas were placed ten centimetres further up, on the centre of our stomachs, but in oligochaetes, the exact segments in which the genital elements occur is normally indicative of which family it belongs to, and can thus be disastrous for the reproduction of an individual who has his genitals displaced.
(4) There is likely a sexually reproducing population in Iowa, at least, and probably in the Sierra Nevada as well, though this may be genetically distinct. Probably, there are many more sexually reproducing populations around the world, but they cannot be told apart from the asexual ones on somatic characters alone. There are 13 more species in the genus, most of which may be sexually reproducing, or perhaps only local asexual ones with aberrant genitals, which is the only character that can be used to tell them apart.
