But this is only for instances of {{reflist}} where there are no additional parameters beyond the refs= list of references, correct? That is, {{reflist}} would continue to exist when being called with any other parameters.

The issue with the removal is clearly a bug (thanks @DLynch for the quick patch).

@Pginer-WMF There is currently a discussion in Wikipedia to convert {{reflist|refs=...}} to <references>...</references> in order to address this. But it would be nice if the VisualEditor were able to remove list-defined references inside <references>...</references>, so that you don't need to switch to the source code editor to fix unused ref errors. T356471 covers both the addition and removal of list-defined references. Fixing the removal looks easier and could be prioritized (potentially by creating a subtask).

For the addition, it could potentially be a big deal, but unlike for the removal it's more about readability than bug fix. It would mean that if there is a list-defined references list, the VisualEditor would put the reference there rather than inside the body of the article. Both placements are valid, but putting references inside the list-defined references list instead of the body may arguably cause less clutter and improve readability in the source code editor. I guess that would be an improvement, but it is a particularly impactful design change, so it probably needs an RfC on Wikipedia to determine if there is consensus in favor of that.

Fixing the removal of references would be really useful. Maybe this could be fixed in priority, potentially in a subtask?