Is it too much trouble to just override the base style with the js style? As in, don’t specify the base style with “no-js” at all, just the js overrides.

Complicates the base case if you need to undo in it any unwanted styled applied in the no-js case.

Conceptually it's a lot easier to manage if they're fully distinct, or at least if the common bits are explicitly common.

most websites are going to be JS-first. If it makes sense for you to augment your site with JS, then sure knock yourself out and reverse it.