Palpatine knew about the Vong before even the Clone Wars:
"What's important right now is that Lord Sidious has access to information sources that the Jedi don't have.""There's an invasion coming," he said. "A massive assault force of dark ships, shadowy figures, and weapons of great power, based on organic technology of a sort we've never seen before. We believe these Far Outsiders, as we call them, already have a foothold at the far edge of the galaxy, and even now have scouting parties seeking information on worlds and peoples to conquer."
-Outbound Flight
Instead of wasting time/effort in helping to construct the Separatist faction as the Republic's enemy, Palpatine could have made the Vong his patsies instead. Granted it would have stalled his plans for several years, but in that time he could have allowed the Jedi Order to continue(so he would have thousands of Jedi to use as his proverbial 'meat shields' against the Vong), and could have also been continuously cloning troops and bolstering his numbers even further... Perhaps even petition to have multiple Death Stars constructed as well.
srug