The alien plan was to interrogate, then execute Tom. It was only Redeye's intervention that saved Tom. There would be no reason for the unspellable aliens to have monkeyed with the testicles of a man they were not going to set free. If the whozis are responsible, it is likely that Hal was the agent and Hal's "probe" the means. However, the only reason as of now for the baby's kidnapping would appear to be as leverage on Tom. Since Hal would himself be leverage or even probably able to kidnap Anne and the baby, it is hard to see what the [slurred vowels and consonants] would bother to engineer Alexis for.
The baby may be a product of Volm interference detected by Hal's "probe" and kidnapped by Karen to foil the Volm plan. The Volm seem to be very committed to a very long war. Improving the next crop of soldiers from allies might strike them as a prudent thing to do.