Brightness/Contrast Difference from PC to YouTube
Looks like Handbrake is outputting full range but flagging it as video levels, so the Handbrake output actually has Y=0 as black and Y=255 as white but the flag is telling Youtube that Y=16 is black and Y=235 is white.

If you upload a short segment (3-5s) of both your Handbrake input and output, that can be confirmed.