Is it normal that the zoom level (or flatten the image) changes the brightness?

I don't think this is about color management. The way the OP describes it is entirely consistent with preview rendering at less than 100% view, on a very noisy image. This effect is well defined and well documented.

Please add your vote to the Cache Level-1 Bug Report. 

https://community.adobe.com/t5/photoshop-ecosystem-bugs/p-impossible-to-set-cache-levels-to-1/idi-p/12248951

It has always been like this. But as I said, you only notice it on a certain type of images.

BTW - this isn't a bug, it's normal behavior (irrespective of whether one thinks it's desirable). Can a moderator move this to "Discussions"?

I just noticed this recently, I don't think it always behaved like this. But yes I mostly notice this in high ISO images.

Yes, you do have a point - but to be realistic, there is no such thing as "accurate" below 100%. Pixels have to be resampled on screen, there is no avoiding that. A group of pixels have to be reduced to 1 single pixel.

Where I do agree with you, and this has been requested many times, is to give us an option to do all preview calculations on the full pixel data instead of the screen sample. The answer we usually get is that this would slow Photoshop down unacceptably. That is probably true, it most likely would - but if it was an option with all implications clearly stated, and it was a one-off, non-sticky setting, I don't see why not.

Many versions ago it was possible to do this by setting cache levels to 1 in Preferences. That is no longer possible.

In a "normal" photograph this isn't a problem. This happens with very noisy or binary data where you have sharp pixel-level transitions. It's these transitions that are averaged out to middle values that aren't really there in the data.

In practice, I live quite well with this, but it's important to understand what's happening and why it's happening.

Even on a 4k screen working 50MP files in 100% to dial in settings is what I would call a "not optimal working situation", usually I would like to see the whole image when doing so and would expect it to be represented accuratly.

Whenever something seems to change when merging layers, it's because you are not viewing at 100%. The merged result is correct. The preview is misleading and incorrect.

100% has nothing to do with size. It means one image pixel is represented by exactly one physical screen pixel.

For performance reasons, all blending and adjustment previews are calculated on the on-screen version of the image. When you are zoomed out, that means a resampled and softened version of the image. Pixel levels are averaged out. You get a lot of intermediate values that aren't there in the full original data.

When you merge, commit an adjustment etc, the numbers are re-calculated on the full original data, pixel for pixel.

Viewing at 100% avoids all this and renders the whole issue moot. You see every pixel before and after, and so nothing changes.