The EG-S doesn't affect spot metering...or any of the metering modes, as long as you change the menu option in your camera.
They don't really do anything wonky in low light though...I may have said something wrong that confused you. Hopefully I can clarify things (without making a mess of it).
The microprisms and split prism only darkens weird (dark bright checkerboard microprism and darkened half split prism) at slower apertures. The slower it is, the more pronounced the effect. And even then, you may be able to reposition your eye so that the effect is minimalized. You can't do that for the rest of the screen (or the eg-s screen) to make it look brighter though.
In low light, it's dark overall, but the microprism and split prism don't darken "weird." Oh, just to clarify, it's not like the precision screen is darker than the stock screen in low light...it's just dark. The precision screen only darkens when using slower apertures.
If you're getting the EG-S screen, you don't need to worry about anything concerning the microprisms, split prism and weird affects slower apertures have on them. Just know that using the EG-S screen with lenses with maximum apertures slower than f/2.8 will cause the viewfinder to appear darker compared to the stock focusing screen.
But, even though it gets "darker", it's really not that bad. I can still see well enough to take a picture manually focusing at ISO 12800 1/25s f/4 (old manual focus lens, so it's stopped down to f/4)...so I don't think you'll have a problem simply looking through the viewfinder at f/4.
I use a 135mm f/3.5 and my 15-85mm @ 85 (f/5.6) in normal light and I don't have any trouble seeing through the viewfinder. Again, because of the slower aperture of these lenses, the microprism collar in particular becomes a little hard to see through, but the rest of the screen (which again, I think, is similar to the eg-s) is perfectly fine.