Yes, it is of course mostly an exif issue, unless exit pupil data get messed up. With 105/4, the compensation would be correct at 1:1.
Edit: No it will not because the 105/4 is not an AFS lens and responds like my AF 300/4 that reports the aperture set on the lens.
I have noticed with TC-14E that there is a tendency for underexposure and perhaps more so with 300/4 PF than AF 300/4. I wonder if that could be due to the lower contrast, or possibly due to different degree of light falloff towards edges wide open in the two models, more so with the 300PF. If the body somehow receives data that compensates for this and there is less falloff with a TC, this would influence total metering.