The updated 2023 vaccine was based on XBB.1.5. In the period you quoted, the variants based on the massive BA.2.86 saltation took over, including JN.1 which was fully dominant by January. XBB.1.5 and BA.2.86 are antigenically very different. I would not be surprised if the case ratio between the two branches during the period was in fact 55:45, i.e. matching the CDC's 54%.
Regrettably, this is one's on the FDA, as XBB.1.5 was already on the way out when the FDA chose it. Part of the problem was their desire to include Novavax in the lineup. It has a much longer update turnaround time than Moderna and Pfizer, and Novavax had already committed to XBB.1.5 by the time the 2023 VRBPAC meeting took place.
As for the original vaccine, the waning measurements were in terms of antibody titers, not in terms of actual effectiveness against the target variant. Delta emerged in the spring of 2021, and it had significant immune escape from WT (Wuhan.) By the time the population was immunized against WT, Delta had already driven WT out.
There have not been many reported cases of non-immunocompromised people getting infected with the exact same variant they had been vaccinated against or previously infected with, particularly with WT. There has been too much evolution in the timeline to even dig out the signal.
The original WT mRNA effectiveness measurements were 92-95% IIRC. For all we know, the missing 5-8% might be attributable to immune deficits, early infections, and/or incomplete B-cell maturation. I haven't noticed any research that measured the likelihood of single-variant breakthrough infection, but if you find some I'd like to look at it.
As for other diseases, they are not in the pandemic phase, so their vaccines can be optimized accordingly.
I would dispute that "easily evolve" notion, though. There have been billions of Covid cases since 2019, including countless immunocompromised patients who are basically walking virus incubators. Yet there have only been a handful of major saltations. It's actually quite likely that Covid will eventually be defeated completely.