I have this same issue since I installed Sequoia. With Sonoma, there were applications that 100% brightness was way too much. But now with Sequoia, there are applications that are too dark even when the display is set to 100% brightness. I find myself checking the brightness setting every time to make sure it's 100%.
The most obvious brightness differences for me are the Apple News and YouTube (via Safari). With Sonoma, the white point in Apple News (using dark mode) at 100% brightness, was blinding and I had to turn down the brightness considerably. With Sequoia, I don't have to lower the brightness at all.
Watching YouTube since installing Sequoia, the videos are often way too dark making it hard to see everything.
I am using a MacMini M2 and the Apple Display. I have checked all my display settings. Auto-brightness is not enabled. I have searched for a solution online and found nothing.