Thanks for the response.
Pixelfed does have a Custom CSS option in the admin panel,
but even with that it's currently not possible to override the logo.
I'm also noticing other things not working. I have filtered registrations
enabled, but I'm not receiving any emails about new signup requests.
And when I try to edit /site/about, the changes don't show up at all.
So it seems this is just the current state of Pixelfed.
Hopefully the developers will fix these issues in future releases.