This is what I believed when I created them. In the case of Megdevi, it came directly from (a) learning about affricates, and (b) realizing that Ancient Greek had the letters ξ and ψ. I assumed they were affricates and phonemes, because they have single letters for them, but they’re not. Technically an affricate has to feature a stop and fricative in the same place of articulation (with some wiggle room allowed on the symbol used for either element. For example, the /t/ part in English /tʃ/ is not in the same place of articulation as our actual /t/). Even so, it seems trivial to take aspirated stops and turn them into stop + [s]—i.e. *pʰ, *tʰ, *kʰ > ps, ts, ks. I’d be surprised if that didn’t happen somewhere, even though actual affricates is more likely (i.e. pf, ts, kx). At that point, they’d be acting like single consonants, because that’s what they were. Still, I think what they’re trying to capture with the idea of the affricate is that it’s a stop with a crazy slow release—so slow that your tongue (or lips) hold on a fricative sound before you let the whole thing go. For that reason, something like Megdevi’s [ps] and [gz] couldn’t be affricates, because no matter how slow you release a [g], you’re not getting to [z]: that takes effort on the part of the tongue.
That said, there are phonemes that begin as one thing and end as another that aren’t affricates. For example, prenasalized stops like [ᵐb], [ⁿd], and [ᵑg], or labiovelar consonants like [kp], [gb], and [ŋm].