I know things like that don’t bother some folks and that’s fine, but others like myself can’t turn the visual parts of their brains off and so some software feels like nails on a chalkboard to use.
That might be the most accurate description of Thunderbird that I've come across. It's hard to pinpoint exactly what's wrong with Thunderbird, despite me using it every day. Somehow it feels like the emails aren't the important bit of the UI, but I also couldn't tell you what I'm looking at instead.
I often find myself in situations where someone wants to break the UI I like, because they're used to something else.
It seems that most of the time, "feels right" just means "it works like I'm used to in other software". So: GMail, Outlook, whatever. Which is sad.
I wonder how would you react to "TheBat!" or Pegasus Mail?
Glancing at screenshots of TheBat! and Pegasus Mail, i don’t find them objectionable in the way I do Thunderbird. They’re just old school desktop clients like I used in the late 90s/early 2000s, which I generally find workable. They’re not quite my preferred style these days (which falls into the “it’s not what I’m used to” bucket you mentioned) but I could probably get used to them again if I had to.
Thunderbird on the other hand feels wrong somehow, and the recent UI “modernization” didn’t do much to change that.