I ran some experiments to investigate the discrepancy.
The largest differences were caused by:
1. A variable quantiser being used for HEVC, but not for VP9 (as you described)
2. Keyframes being forced every 30 frames for VP9 in the first paper
HEVC also had I frames added every 30 frames, but these were not IDR frames, meaning that B frames were allowed to use the information from the I frame in HEVC.
However, in VP9, true keyframes were forced every 30 frames. The way VP9 works this meant that every 30 frames it encoded both a new Intra frame, and a new golden frame.
Making both codecs use a true fixed quantizer and removing the forced intra frames made the results more like Google's own paper.
I guess the moral is to not force frequent keyframes when encoding with VP9.
The largest differences were caused by:
1. A variable quantiser being used for HEVC, but not for VP9 (as you described)
2. Keyframes being forced every 30 frames for VP9 in the first paper
HEVC also had I frames added every 30 frames, but these were not IDR frames, meaning that B frames were allowed to use the information from the I frame in HEVC.
However, in VP9, true keyframes were forced every 30 frames. The way VP9 works this meant that every 30 frames it encoded both a new Intra frame, and a new golden frame.
Making both codecs use a true fixed quantizer and removing the forced intra frames made the results more like Google's own paper.
I guess the moral is to not force frequent keyframes when encoding with VP9.