Well, I think that's a big part of the issue. f-number (not the same as actual aperture), shutter speed and ISO all affect the brightness of an image. So it is fair to think of them as some triangle where they all play an equal role in a sense.Doesn't the exposure triangle stay the same? By that I mean ISO, shutter speed, and f/stop? Cropping may well change the "bokeh", but doesn't change the aperture or the exposure. Other than that, I got nothing. As far as noise, I almost never go above ISO 400 anyway, though I am sure others go way beyond that. So maybe I'd be better off saying, "for me."
But f-number and shutter speed control the amount of light that contributes to your exposure. ISO is different than the other two - it merely amplifies what the other two determine. Therefore, thinking about it as equally important as the other two can lead to confusion.
For example, people associate ISO with noise, when in reality, the noise in your image is almost entirely determined by f-number and shutter speed, or the signal in your image. ISO just needs to get higher when the others are to low to achieve the desired brightness. But it is not responsible for the noise. In fact, higher ISOs show less noise if you keep the other two settings identical and adjust the brightness in post to match between different ISO values.
So it doesn't really matter if you stay at or below ISO 400 all the time. If you push the brightnes of your image in post, that is the same or worse than shooting at a higher ISO.
And as cropping discards light from the edges of the frame, any noise in the image will become more apparent. Doing the crop in hardware through a TC and adjusting brightness via ISO or editing delivers a very, very similar image. So, the only difference between TC and crop comes down to resolution. You lose some quality due to extra glass in a TC. And you lose a bunch of pixels when cropping. Depending on the resolution of your sensor, one will be better than the other.