In an application for a visa, does the UKVI accept a cover letter to explain anomalies/disparities between two applications?
The visa application form contains a free-form field (part 9 in the paper version) for stating any other information you wish to be considered as part of your application. It instructs you to use additional sheets if the form itself does not have enough space for everything you want to say.
This will be an excellent place to explain changed circumstances since earlier applications, or the relationship between applications in general.
(I imagine the online application process is similar, but it seems to be impossible for a member of the public to see exactly how that goes without entering an email address and fradulently claiming that I'm intending to apply for myself ...)
Don't format it as a "cover letter", though -- that would just create a risk that a confused clerical worker somewhere removes it from your application before it gets seen by an ECO.
Yes (they can hardly refuse to do so when sent as part of a package that they do not know contains a covering letter until they have accepted the package and opened it).
Will they read it? Probably, if it is brief.
Will they heed it? Rather depends upon its content.