These just seem like standard MP3 album files with “pause” included in end of file, as on all digital albums AFAIK. What you’re seeing to the right of the playbar in iTunes is a countdown of the entire file (not a switch from count-up to count-down as on CD) and the last 3 seconds of “silence” are just counting down to end of file.
If you open the files in Wavelab or listen in headphones, you can see there is room noise out to the end of file. If you look at the metadata of the file in Wavelab or MP3Tag, there are no markers indicating where to “start” a pause, which would be the only possible way to do this, but would probably be of no use on most players, which is why this is never done as far as I know. The only place I see in Wavelab metadata to add markers is in CART, but that’s not used in MP3 or AAC.
As far as I know, what you have been told is correct: “pause” is added to the end of file, and there is not a “CD like Index 0 Index 1” corollary in the commercial digital file music album world.
I’ve heard of MP3/AAC chapter markers, but that would be a different usage.