hawkeye : continuum's interpretation is correct.
In fact, what happens in the 12 sound couples present in this sample, is that they are made of the last N (N= 2, 3, 4, ...) harmonics of different fundamentals, up to the LCM of the two fundamentals. But they never include the fundamental harmonic.
So the lower frequency the fundamental, the lower the distance between its harmonics.
Because of this, as the LCM (the higher band on the spectrum view of both sounds) is the same, the frequency of the N harmonics just before LCM are higher for the lower frequency fundamental than for the higher frequency fundamentals.
So the sound which has the lower fundamental (the fundamental is the GCD of all the harmonics) has the higher N harmonics before the first common harmonic (which is LCM of the fundamentals of the two sounds).
(LCM = lowest common multiple, GCD=greatest common divider)
For example, take couple number 12.
(I used audacity, hence the screenshots are from it.)
Its spectrum is

The first sound (left) is made of two bands: the lower, around 1328 Hz, and the higher, around 1660 Hz. They are separated by 332Hz.
1328=4*332 and 1660 = 5*332, so these two bands are respectively the 4th and 5th harmonics of the fundamental 332Hz (332 is the GCD of 1428 and 1660). This corresponds almost to a E2 (E2=329,63Hz).
The second sound (right) is also made of two bands: the lower is around 1245 Hz,and the higher is around 1660Hz as for the first sound.
1245 = 3*415 and 1660 = 4*415. These two bands are respectively the 3rd and 4th harmonics of the fundamental 415Hz (415 is the GCD of 1245 and 1660). This corresponds almost to a G#2 (G#2=415,3Hz).
The harmonics of the fundamental of first sound (332Hz) and of the second sound (415Hz) join at 1660Hz, as 1660 is the LCM of 332 and 415.
A fundamental tone hearer interprets the first sound as the 4th and 5th harmonics of the fundamental at 332Hz, a somewhat detuned E2, and mentally reconstitutes the missing fundamental. Try hearing the first sound of the 12th couple and playing an E2 on an instrument.
After that the fundamental tone hearer interprets the second sound as the 3rd and 4th harmonics of the fundamental at 415Hz, an almost perfect G#2, and mentally reconstitutes the missing fundamental. Try hearing the second sound of the 12th couple and playing a G#2 on an instrument.
As you see the fundamental hearer hears the second sound higher than the first in the 12th couple.
An overtone hearer interprets the first sound as the combination of two sounds: a pure harmonic at 1328 Hz (a slightly higher E4) and another pure harmonic at 1660Hz (an almost perfect G#4).
After that the overtone hearer interprets the second sound as the combination of: a pure harmonic at 1245Hz (an almost perfect D#4) and the same almost perfect G#4 at 1660Hz.
As you can see the overtone hearer hears, in both sounds, two notes, one of which is lower in the second sound (the D#4) than in the first sound (the E4).
--- A second exercice: how to hear like an overtone hearer when you're fundamental tone hearer and vice versa ?
A) you're an overtone hearer and wanna understand.
Create a sound which implements all the harmonics of the fundamental, including the fundamental and, of course, the two that you hear as distinct sounds.
Here, I created a sawtooth signal of frequency 332 Hz (E2), followed by the first sound in the couple 12 of the test, then a sawtooth signal of frequency 415Hz (G#2), followed by the second sound in couple 12.
Sorry, no flac, just a
mono WAV file.
The spectrum is as follows

You have the kind of signal that a fundamental tone hearer reconstitutes (timber excepted), down to the fundamental tone (lowest bar in the "ladder").
B) you're a fundamental tone hearer, you wanna understand (as me)
Create a sound separating the two components of the sound couple 12.
Here is a sine signal of frequency 1328Hz (the E4), followed by a sine of frequency 1660Hz (the G#4), followed by the first sound of couple 12, which is their combination.
Then, a sine of frequency 1245Hz (the D#4), followed by the same G#4 at 1660Hz, followed by the second sound of couple 12, which also is their combination.
Here again, no flac, just a
mono WAV file.
The spectrum is as follows

You have the decomposition that an overtone hearer gets.
Amusingly, when performing that second experience, I had difficulty returning back to my 'fundamental tone hearer mode' on the sample ! (talk me about rewiring the brain)
Note : as I'm a fundamental tone hearer (12/12), I'm not sure the example sound in A is well suited for overtone hearers. I myself don't hear the different sounds composing the harmonics. But I can, with exercice B. One of my coworkers heard the distinct frequencies, and still managed to get 12/12 when I asked him to search the fundamental tone. Great !
Hope it helps a little. All in all, I lost a nice day

.
Vincent