<blockquote>
<p>both the Egypt and Eritrea boundary relations were fine according to JOSM validator.<br>
So why were those missing as well? Is this a potential issue in osm2pgsql, or an issue with the Africa extract?</p>
</blockquote>
<p>my suggestion:   check the "Africa extract" first,</p>
<p>For example Eritrea  - Geofabrik extract Poly - smaller than the   admin_level=2   border<br>
<a target="_blank" rel="noopener noreferrer" href="https://user-images.githubusercontent.com/2217320/55902217-5390d480-5bcb-11e9-93ea-aeb03a272f44.png"><img src="https://user-images.githubusercontent.com/2217320/55902217-5390d480-5bcb-11e9-93ea-aeb03a272f44.png" alt="image" style="max-width:100%;"></a></p>
<p>And the same - in the Africa Geofabrik extract Poly.<br>
<a target="_blank" rel="noopener noreferrer" href="https://user-images.githubusercontent.com/2217320/55902556-137e2180-5bcc-11e9-8e3c-35e6b9f265f7.png"><img src="https://user-images.githubusercontent.com/2217320/55902556-137e2180-5bcc-11e9-8e3c-35e6b9f265f7.png" alt="image" style="max-width:100%;"></a></p>
<p>imho:  for the borders ( admin_level=2 )  - the planet file is the best.</p>

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