I think they prepared both PDFs and then tweaked with bits in both of them. This is much easier than tampering with only one PDF.
So I think it's still very hard to generated a CA cert where you can just copy the signature of an existing cert.
But maybe you can predict exactly what parts from your signing request and what timestamp and serial number and so on the CA will use, then you can maybe precompute a signing request that will result in a cert where you can replace some parts with other, evil, precomputed ones.