To clarify your learning experience, try the following out for size: The darker trees are closer to black than to the mid tone you incorrectly assessed them to be. That incorrect assessment also made you erroneously think the histogram is incorrect, when in fact it is correct. Even so, the darker trees are not so close to black that you would have risked clipping the shadow tones if you had reduced the exposure a reasonable amount for whatever reason you might have had in mind.
Considering that the highest luminosity value is 255 and that the brightest tones in the image are at 253, you should expect the far right side of the histogram to indicate that some tones are almost clipped. I don't understand why you would think otherwise.
Such a small display of the histogram, whether it's the histogram displayed in the camera's LCD or the histogram displayed in Lightroom, makes it difficult if not impossible to accurately assess such fine details. If CiC's tutorial is correct that you can usually retrieve during post-processing about 1 EV of clipped highlights or shadows, there is no need to be concerned about any further detail when reviewing a histogram.
First, keep in mind that you used matrix metering, not spot metering, when capturing the NEF that you provided to me.
Second, you would only spot meter a relatively bright tone in the image if you also plan to increase the exposure beyond the exposure the meter would otherwise indicate to use. When using spot metering, I'm reasonably confident the camera "thinks" the luminosity value being metered is 128 (the very middle of the mid tones), though more technically-minded people who unlike me regularly use spot metering may correct me. Another way of putting it is that whatever luminosity value you choose to spot meter, the camera "thinks" it is the same luminosity as a grey card designed to be used for metering.
Every time you mention that, I cringe.
Even if that statement was true, it does not indicate that using exposure compensation combined with matrix (evaluative) metering is ineffective. All I can tell you is that 99% of my photos are made using matrix metering and exposure compensation and they are metered to produce the exact exposure that I wanted to achieve. If that's ineffective in Nikon's mind, so be it.
That makes sense to me. It also contradicts your earlier statement that the process of using exposure compensation in manual mode doesn't involve changing the aperture or shutter setting.
That also makes sense to me. That's because once I have chosen the Manual mode, it doesn't make any sense to me to then use an automated method such as the Exposure Compensation; it seems both natural and faster to fine tune the exposure manually.
No, that is not a contradiction. Read the Nikon information again. It clearly states that the resulting display of -1 EV on the scale indicates that your shutter and aperture settings will result in an exposure that is 1 EV less than what you want (less than what you have set the exposure compensation to). That -1 EV is NOT indicating that the camera has automatically adjusted the exposure; it can't do that automatically because it is in manual mode.
I'm compelled to note that part if not all of your confusion has surely come about because you are trying to master spot metering, matrix metering and manual metering when it's clear from your posts that you haven't mastered any of them. Your chosen course of action is NOT working for you, Christina. Personally, I can't justify taking the time to continue going over and over this stuff when I see no end to your confusion so long as you pursue trying to master all of them at the same time.
Do what you want, but I strongly recommend when shooting landscapes that you master matrix metering combined with exposure compensation before moving on to any other method of metering.