The first really important question is what exactly it means that those countries use ivermectin or are part of APOC. Both papers seem to assume that this status is binary, a country is either in the ivermectin/APOC group or not. But what exactly does this mean for the use of ivermectin in both groups?
APOC is the WHO African Programme for Onchocerciasis Control. I'm using the final report for this program to try and understand what exactly defines this group of countries the two papers are examining.
One important first aspect is that APOC has been finished in 2015. So this does not describe any current efforts, but a past program. Another important question is how much ivermectin was actually distributed. If ivermectin were the cause for the discrepancy a very large percentage of the population would have to be taking ivermectin. The first paper states an almost 10 times higher rate of death due to COVID in the non-ivermectin group, such a huge effect would not be possible if only a very small percentage of the population take ivermectin.
One page 24 of the APOC final report you can see how many tablets of ivermectin were distributed. At the end in 2013 this was 225 million per year for all APOC countries combined. Using the data in the first paper, the total population of all APOC countries is 972 million people. Acoording to this PLOS paper a treatment of ivermectin is 2.8 doses on average, and the estimated number of treatments was 92.5 million.
So only about 10% of the population in these countries were actually treated with ivermectin under this program. This does not seem enough to explain the dramatic difference the two papers state. And keep in mind this data is outdated, it might be even lower today.
Another huge potential confounding factor is the accuracy of the data for these countries. The number of tests varies dramatically between countries, the data is simply not directly comparable:
Presently, no country or continent knows the total number of people infected with COVID-19, despite the confirmed cases. The counts of confirmed cases largely depend on how many people have been tested in each region. To properly monitor the spread of the virus, countries need widespread testing. The African region has about 1.2 billion population, and about 2.4 million people have been tested for COVID-19. However, the continent has a testing target of 8000 tests per million population [3]. South Africa has conducted 54, 224 tests per million population, with Egypt conducting 1, 317 tests per million population and Nigeria conducting 1, 504 tests per million population [4]. Among European countries, the UK has conducted 266, 500 tests per million population.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7485446/
If a country has performed 40 times as many COVID tests per population than the country you're comparing it to, you won't get any useful data out of this comparison.
Drugs also don't stay in your body forever, so the number of people that had taken ivermectin just at the time they are also getting infected with COVID is much smaller.
The plasma half-life of ivermectin in man is
approximately 18 hours following oral administration.
https://www.merck.com/product/usa/pi_circulars/s/stromectol/stromectol_pi.pdf
The half-life of ivermectin is 18 hours, so after a few days there isn't much left of it.