LiveView ISOs are a little lower than displayed.
I've measured 82 on 5D3 LV, vs 104 in photo mode - that is, 0.34 stops difference.
You took the CR2 at F1.4 (from exif), and at this aperture,
Canon applies 0.15 stops of digital gain (found by DxO and confirmed by my experiments - the exact value is log2(0x239/0x200) from the
digital gain configuration).
So, you should expect the MLV to be 0.5 EV darker than the CR2, assuming identical metadata.
I've converted your CR2 into DNG with Adobe DNG converter, so ufraw renders it like any other DNG (that is, normalizing the raw data according to black and white levels from metadata, and not other black magic), and I still needed 0.45 stops of exposure compensation for the MLV.

Noise levels are obviously going to be different (see the first link). The 5D3 does
hardware 3x3 binning on the sensor, and then it adds read noise from its electronics (after binning). The end result is worse than a CR2 downsized by 3x3 in software, both in sharpness and noise levels.
=> this is not a bug in MLV.