Well, yes -- but given that we're talking about the insertion of a very specific human gene, the likelihood of it being there due to "bacterial conjugation [or] viral insertion" is rather tiny.
I ask you to provide an example of a phenomenon studied by science in which the supernatural explanation has provided the better explanation.
Why are we suddenly talking about supernatural explanations? You've shifted the goalposts.
ID assumes a designer other than natural selection. There is no naturalistic reason to make such an assumption. No deficiency has been pointed out in the current mainstream precedures and methods of science.
If it isn't the spaghetti monster, what is it?