Unfortunately this is a case where we'll have to agree to disagree. Half the time with Electron apps I wish I could disable CSS completely and just use my system theme because it sucks less than whatever the designer came up with for that app (the definition of "sucks less" falls into many axes that vary per application and context; no point in digressing far into that), so what you described would be a feature, not a bug, to me.
(Further, I basically never, ever want an app to theme itself. Ever. If I set a system theme it's because I want the system to look like that. I've gone on tirades here and on other forums for years about finding https://stopthemingmy.app/ and even just the freedom of every electron app to pick its own HIG and UX as absolute heresy, so if nothing else, my opinions are consistent here.)
I couldn't agree more, unfortunately we are a minority :(. Before react was mainstream, you could "fix" websites pretty easily with things like greasemonkey, but even that is super painful now. CSS modules mangle classnames, so every new version (which are pushed multiple times per week/day) will break your naive css modifications. You can't naively modify DOM elements because React will overwrite them almost instantly.
I know you can write regex in your CSS selectors and use MutationObserver's to update the DOM after react and co are done with it, but it's just so much more painful. Something that used to take maybe 1-2 hours to get some site working/looking how you like it, is now a part time job.
This is what really bugged my about “portable” Java apps way back. Java Spring was especially noticeable. It stuck out like a shore thumb compared to the regular system UIs.
Some like Magic User Interface for the Amiga, but across Operating Systems, and which provides the resulting stylesheet to the browser (with no ability for sites to override it unless I allow it) would be my dream and a marketers nightmare. Just information and media, displayed how each person prefers them to be displayed (and obviously with a lot of user made themes for people to browse and try out). With sub-configs like super-compact, whimsical etc. that users can apply to individual apps and sites.
(Further, I basically never, ever want an app to theme itself. Ever. If I set a system theme it's because I want the system to look like that. I've gone on tirades here and on other forums for years about finding https://stopthemingmy.app/ and even just the freedom of every electron app to pick its own HIG and UX as absolute heresy, so if nothing else, my opinions are consistent here.)