Yes, it had layers, but is there evidence that this was done by Obama’s staff working from a genuine BC?
Yes, although the "genuine" BC was a certified copy from Hawaii. There was a document sent from HI, and the document was a certified copy of Obama's BC as noted by numerous witnesses and confirmed by HI. But between that document removed from the envelope and PDF posted online any number of things could have happened. Occam's razor explanation was simple layer creation from a scan.
Alternatives are rather meager. The main one is PDF created from another person's BC with altered names, etc
PDF created from the document sent from HI is far simpler.