Yep, I had the same experience, but it's trivial to disable DR for a domain, so I wouldn't put much effort into it.
Tesseract
Tesseract: An Advanced Lemmy Client
The goal of Tesseract is to address as many things in Lemmy that annoy me as I can. I also trawl various "is there any way to [blank] in Lemmy?" posts to get feature ideas. Both of those lists are pretty extensive, so Tesseract has accumulated quite a few features.
Github: https://github.com/asimons04/Tesseract/
Hosted / Demo Instance: https://tesseract.dubvee.org
Note that the hosted instance defaults to Lemmy World, but it is unlocked to be able to connect to any Lemmy server.
Announcements, support, and guidance for the Tesseract UI.
All instance rules apply here. Beyond that, just be civil and constructive.
Somehow DR got re-enabled for me in dev after I had just made some tweaks to the Tailwind config. Freaked me out for a minute because I thought I royally screwed up Tailwind lol.
Does dark reader detect if you add CSS specifying that it's a dark theme? No idea if it does, but maybe something to look at.
I also thought Tesseract had some odd theming choices until I remembered I've got DR installed lol
Ok, I looked into it further, and I can actually just have the app ask Dark Reader to disable itself: <meta name="darkreader-lock">
Added that in dev, and it works.
There are already CSS classes in place which say it's in "dark" theme, but DR doesn't look at those. They maintain a list of sites that are already natively dark that it will ignore, but that's impractical for a Fediverse application which can be hosted on any domain.
I hate to be heavy handed about it, but there is a dark theme already that also responds to system preference (in addition to having easy-to-reach manual toggles). There's a way to do it dynamically which I may work on, but it'll require additional testing.