[El Gato]

Indentions in the document are hard to pick up by scanners since they usually don't change the color or shading of a document very much.

Funny then that they show up fine in other Certifications of Live Birth posted on the 'net. Such as this one:

Or this certified copy of a Certificate of Live Birth (it's a little hard to see on this one, but it's there in the upper right, starting near block 7c.

[curiosity]

Not all scanners are equal. Some are better at picking up subtle changes than others. Some have higher resolution. Some have higher contrast ratios.

Then there is the issue of how forcefully the seal is indented into the document. In some documents it is punched more strongly than in others, so that in some documents a scanner will be able to pick it up, and in others it won't.

The above is obvious from the two images you posted. In the first one, the seal comes through very clear. In the second one, it comes through just barely. If the scanner used had been set to only a slightly lower resolution, or if its seal were punched with just a little less force, you would not be able to see its mark.

At any rate, in the photos of Obama's certificate, the seal came through just fine, so this is a moot point.