Yes, JPEG engine is responsible.
To be honest I don´t care who is responsible for waxing. X-Pro2 has option for switching off the waxing and that´s enough for me. So now I have to wait for X-E3 and I will completely skip X-Trans II generation cameras including X-E2s.
So hopefully Fuji solved waxing issue:
http://jonasraskphotography.com/2016/01/15/the-fujifilm-x-pro2-review/
The reason why I sometimes still pull out my X-Pro1 (besides from the OVF experience) is the ability of the X-Trans I sensor to render high ISO jpegs without the excessive noise reduction that the X-Trans II cameras apply at these high ISO values. The result of this noise reduction is the dreaded “waxy skintones” problem! – Fujifilm solved this issue as far as I can tell in my testing. I have had zero “waxy skintones” even at ISO 10000! – You can actually also set the noise reduction to -4 now instead of -2. THANK YOU Fujifilm!