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You are basically right, except I think the technology is 2011 — run out to Staples and buy an all-in-one for $150 or so — not decades-old raised floor stuff. The White House PDF is very likely a scan of a paper document hand-carried from Hawaii and done on standard office equipment by a non-expert in document processing.

The PDF format format was released in 1993, when the technology was still feeble but rapidly improving. But they didn't get rid of all those cool document optimization algorithms just because the computers got orders of magnitude more powerful.

If you scan a normal document to a PDF on a normal office scanner and then examine it, you will see effects quite similar to what are seen on the Obama document. In fact, even when simply viewing a multipage document you will often see the text and background paint on the screen at slightly different times.

Here's what Nathan Goulding wrote in the National Review back when the document was released and the layer controversy got started:

The PDF is composed of multiple images. That’s correct. Using a photo editor or PDF viewer of your choice, you can extract this image data, view it, hide it, etc. But these layers, as they’re being called, aren’t layers in the traditional photo-editing sense of the word. They are, quite literally, pieces of image data that have been positioned in a PDF container. They appear as text but also contain glyphs, dots, lines, boxes, squiggles, and random garbage. They’re not combined or merged in any way. Quite simply, they look like they were created programmatically, not by a human.
What’s plausible is that somewhere along the way — from the scanning device to the PDF-creation software, both of which can perform OCR (optical character recognition) — these partial/pseudo-text images were created and saved. What’s not plausible is that the government spent all this time manufacturing Obama’s birth certificate only to commit the laughably rookie mistake of exporting the layers from Photoshop, or whatever photo editing software they are meant to have used. It’s likely that whoever scanned the birth certificate in Hawaii forgot to turn off the OCR setting on the scanner. Let’s leave it at that.

They don’t know how document processing worked in the past, thus they don’t understand what they’re looking at and can only explain it as “conspiratorial”. Should this ever reach court, they risk a very embarrassing & effective legal smackdown as a result.

If the question ever gets a proper court hearing, they will introduce the true original from the Hawaii DoH. More than likely, it will not differ in any material way. At that point, the game will be up. Then the Sheriff will have claim the fraud happened not via forgery but via misrepresentation in 1961 (or maybe he'll try to prove it was a DoH inside job). Good luck with that!