Thanks for the feedback! There never was an explicit dark theme option, instead CSS system colors were used to provide this effect. Unfortunately, Firefox disabled that feature in version 61+ so it's always been defacto hard-coded to black-on-white since then.
Thanks to your suggestion I have already implemented a working prototype that will instead automatically adapt to the color of the currently enabled theme. I hope to publish that soon.

There was a problem with Waterfox/FirefoxESR. This has been fixed. Please write a new review if that is not what you meant.

Возникла проблема с Waterfox/FirefoxESR. Это было исправлено. Пожалуйста, напишите новый отзыв, если это не то, что вы имели в виду.

> The huge size of the drop-down menu.

This was added a couple of days ago to compensate for people with high-res monitors where the popup ended up being tiny. I guess it will become another option in settings…

UPDATE: Reverted to the previous behaviour, the new behaviour is now available as a disabled-by-default checkbox in the extension options.

> The huge size of the extension itself.

Since this is a recurring question I've added an FAQ entry to the extension's description. Please kindly refer to that for an answer.

> Access to browser activity during navigation.

Used to switch the extension's icon color and tooltip when you navigate from/to pages that have an override set. I could do without that permission but this way it is more reliable and easier to implement (note that extension will be able to see all sites you visit regardless of this permission, it's just more convenient to do it this way in this particular case).

Sorry for the inconvience caused by the recent changes. Version 1.3.4 should now stop the remaining breakage from occuring. If you still observe issues please send some examples of broken sites and what is wrong with them so that I may take a look. Thanks!

While I will not comment on the content of the websites you mentioned, I've fixed several issues on these sites with 1.3.4 that at least made Twitchy & Breitbart work. The Hill I could not test as their page is deploying a security policy that prevents access to all external resources (including Disqus) and hence is broken either way.