Five minutes with emacs:
showed me that the layers are arbitrary junk, not careful forgery requiring hours of work to analyze. The arbitrary junk comes from the fact that the layers were separated with thresholding with darker text in one layer and lighter in another. That's why R in BARACK is in one layer and "BA ACK" in another. Simple explanation for the separation is that someone separated it. Whether the original was a forgery or fraudulently created in Hawaii or legitimately released in Hawaii is unknown, but the layers are not evidence of anything other than post processing.
The best explanation of why someone would post process is a "rope a dope" exercise. Donald Trump will now look like a dope since real reporters have held and touched the original paper artifact that was the source of the WH PDF with the layers. Granted the one reporter I know about is a ditz who did not look carefully at the raised seal and took a low quality snap (probably with her cell phone). But again that fits the theory that the WH is trying to make the birthers look like they are stupidly ignoring reality. And so far they are succeeding to an extent.