When looking at the today's featured article on en.wp there are numbers + letters for the citation.

https://en.wikipedia.org/w/index.php?title=Ai-Khanoum&oldid=1131075173#Citations

Please provide more information in which context you see letters + letters

Preview of an edit? VisualEditor edit? Older MW version? etc.

So with the now linked example I can see that the on-wiki css changing the list-style-type to lower-alpha resulting in use of letters.
That is part of the Reflist styles in https://en.wikipedia.org/w/index.php?title=Template:Reflist/styles.css&oldid=1011085734

Seems nothing the extension can take care of.
Maybe the extension has to provide some classes to allow styling of the "a b" links, but I have no idea how that has to look, that on-wiki css can change it as well.
Defining these backlinks as list (<li>) needs a check if that could make problems with accessibility.

Currently the backlink is a static text. That means that the issue cannot be solved with styling. The easiest fix would be to output numbers instead of letters for backlinks in groups like lower-alpha.

The extension does not know about group names like upper-alpha, upper-roman, lower-alpha, lower-greek, lower-roman and its special styling on en.wiki. It cannot output difference things when it does not know about that.

These are indeed replaced using CSS, although they're static text as you pointed out. The rule is using content to replace text.

See for example this snippet from English WIkipedia Common.css , which is responsible for adding the letters in the first place:

span[ rel='mw:referencedBy' ] > a::before {
	content: counter( mw-ref-linkback, lower-alpha );
	font-size: 80%;
	font-weight: bold;
	font-style: italic;
}

The basic idea is that you'll want to write a selector which only applies to backlinks inside of a list using letters, then revert back to content like counter( mw-ref-linkback, decimal ).