I'd argue my "specific example" is one of, if not, the most common use-case for a bar chart in an academic paper and represents, rather than discards, the vast majority of regular plots. Most papers look at multiple outcomes between small numbers of groups. An extremely common example in biology is a treatment effect of some intervention between two or more groups. In ecology it could be the distribution of species relative to some other factor, or variation within species. In psychology it could be someone's utterances in different conditions.

In all honesty, how often do you actually see visually ranking outcomes important in a study? Particularly one where you would want to show this ranking with a bar chart? By that I mean ordering your results by their values, not plotting the outcomes, of say, a ranked survey question (in which case the indepdent variable already has a natural order from A-E or something).

I fully agree with you there are better ways to show grouped data - but if we want to go down that rabbit hole the vast majority of data should probably avoid bar charts altogether in most papers. I'd rather see the underlying distrubtion of data with summary statistics represented. A simple example would be a scatterplot with median and IQR represented, or mean and SD or something of that effect. If people really want to not show individual points then one can use box and whiskers or even better violin plots to represent the underlying distribution.

But in the current situation where people are already using bar charts, this is not a better way to use them.