That's not how it works. it is "on top" of the previous, sure, but the same way as if I add 8 to 2 and give you 10, you can't possibly get the original number is 2.
Let’s say you’re covering a red pixel with a black pixel. There’s no way that red pixel will in any way “survive JPEG compression” because the compression happens on the raw pixel data; the raw pixel data no longer has a red pixel.
They're saying that before encoding the red dot could have been X pixels wide, and to the naked eye it would seem that after encoding it's still only X pixels wide... but due to compression artifacts it may now actually be affecting an area X+Y pixels wide. So only covering X pixels could leak Y pixels of information.
It honestly sounds a bit paranoid to me, but it's definitely possible.
This is trivially untrue for JPEG; JPEG often stores chroma info as 4:2:0, that is at a quarter the resolution of luminance info. In this common case, covering a single red pixel in the decoded form only removes a quarter of the chroma information from its presence (and this is easy to not notice if, for example, the other three pixels that share its chrominance are nearly black).