Instead of emitting a CSS counter reset for each footnote marker, the WMDE Technical Wishes team is recommending that we emit literal text such as "[1]". This makes it possible to do localization and alternative counter markers as part of programmatic document rendering, makes it simpler to implement "extended" subreferencing, simplifies the output markup, and improves consistency when copy-pasting article content.
On the flip side, CSS customizability has some strengths, so we would like to leave the question open for discussion before making technical changes.
Breadcrumb: this style of numbering was first introduced in {T86782}, but from my brief investigation it was never implemented this way in the legacy Cite parser (thus on-wiki display is not *yet* dependent on the CSS counters), and the problem being worked-around in 2014 was that Parsoid was written in JS and so didn't have access to the PHP localization infrastructure.