Hey Rekrunner, forgive my slow response...
I found it interesting that out of the whole 20-year period, the 2001 year of these events was often the slowest. I expected more variability and that there wouldn't be such a clear chronological trend in most events. The purpose of the trend analysis is not so much a search for causality as it is to determine the natural range of variability and improvement that each event exhibits over time. For that reason, I would say the more years, the better.
(It also became clear that each event's performance timeline needs to be examined on its own. It was surprising, for example, that the trajectory of the women's 10000m was quite a different shape than the 10K Road race, which I can't explain.)
That said, I do wonder if there is some artifact in World Athletics data due to sample size or some of the other factors you mentioned that explains the trend, rather than actual changes in performance. For example, if WA was regularly pulling the times of past dopers as they became aware of them, that would have the effect of dragging down the average in previous years compared to the present. But it seems like even banned runners still have their times included in these historical datasets.
The research on running efficiency showed that, although there was some variability, all the runners that tried the shoes in the lab showed relatively massive gains in performance (around 2-6% over the Adidas Boost). Thus a 2% increase in speed (from a 4% increase in efficiency) should have been the *average* boost observed in all of the top runners that wore them. I could see how a field of runners in a race of 100 participants might contain some non-responders, but these top-100 were all having good days. The common idea that it's only the record breakers and outliers that are benefitting from the shoes just isn't supported by the research, or even by anecdotes.
No doubt much of the difference in performance is due to the changed circumstances of the races as you describe. I'm not arguing runners of today are actually that much faster than ~20 years ago. But the adoption of the super-shoes was, relative to other factors, sudden and clearcut, and should have generated an obvious signal. The difference between the slowest and fastest times in the men's marathon has been about 5 minutes, or ~4% of the total time (for women, about 10 minutes or 7%), so if they were all wearing the shoes, the entire list of runners should have moved halfway up the page! The only reason that wouldn't have happened, of course, is that not everyone wore the shoes early on, but now we're over 90%.
You're right, though, that if 2021 was still not back to normal from the elites' perspective after the pandemic, that could have affected times upward significantly, and maybe we'll see big moves downward in the years to come that could be explained by the shoes. But I would bet against it.