Do that if you want to average the light that is falling on both sides of the subject (i.e., from the area covered by the dome). But when using light that is uneven, why would you want to average it as a matter of course? Sometimes you do, yes. But not always; not even often, I would say, for my own pix. Do this in deliberate ratio lighting, e.g. a side-lit portrait, and you overexpose. The more contrasty the lighting ratio, the more overexposed you will be.

Point it at the light for which you want to correctly expose - the "main light." You have gone to all this trouble to craft light, or choose a location and time of day, that will sculpt the subject the way you want it, why would you then average that light with the dark side, which you have intentionally made dark? You crafted, or chose to use, the light that way because you want the dark side to be dark. If you don't want it to be dark, then change the fill ratio. Don't average the exposures for the light side and the dark side as a matter of course; it does not make sense. For best results, one meters the main light source, unless in very flat, even light, in which case one could point the dome practically anywhere and get the same reading.

Y' pays y'er money and y'er takes y'er choice.

Yes, there ARE areas of the scene that I would want "dark", but the question is "How dark?"

If you measure ONLY for the Main, you wil get ... a density in the negative that correlates to 18% gray, and the "dark" areas will sink into some level of unmetered black.
All well and good, if you are a devotee of "It ain't good unless there is a *really* dense, black area".

It depends .. on the situation, the intent, the aesthetics (aesthetics - there is a cop-out).

Generally (read: exceptions would not be surprising) I would use out-of-the-box `Set the meter and dome to "Incident": At the subject, point the meter more or less at the camera' and blaze away.

Experience helps - a LOT.