Your D800 really should autofocus in Live View - how well it focuses will be a matter of great discussion. We know LV AF is slow compared to VF phase detection AF.
You mention taking example photos at close range. We have to observe the lens closest focusing distance. The lens that I used in example photos below has a closest focusing distance of 4.9 ft. My example shots are at about 5.5 ft. I'm presuming from your mention of a pink rose against a green background, you're not shooting macro.
>The images come out darker if taken in live view. Is this normal?
Not necessarily, and not with the example photos with my D800 shown here. These examples are a VF shot followed by two LV shots - one AF and one manual focus. All photos were shot with Matrix metering and Auto-ISO. So in this particular series, only the ISO level varied. The LV ISO levels are slightly higher, so the image is a bit lighter, not darker. Shutter, aperture, ISO data are all included in photo descriptions in my gallery.
I've done some other comparison of VF to LV metering in all three metering modes. From what I've seen so far, metering in LV with the imaging sensor behaves pretty much as expected. And does not vary wildly from results obtained with the VF metering sensor.
LV excels at providing a magnified view of the subject for focus. Then lots of folks with good eyes like to really zero in with manual focus.