Hi,
I just thought of something: since Flatpak uses a sandbox, that could be the cause of the absence of VDPAU in Kodi?!
So, because I'm curious 
, I installed Kodi from Zorin source (18.6) and then from Kodi ppa manual install (20.2) and yes, hardware decoding options are here (with both versions) unlike the Flatpak version!
These are the hardware acceleration options which was missing in the Flatpak version:
Very happy, I hasten to activate the MPEG-4 VDPAU option and test a video in this format 
.... and... 
, Kodi still using the CPU to decode the video...
I am trying to install vdpau-driver-all but if I understand correctly it is already installed:
I installed vainfo which tells me VAProfileNone 
While doing research I tried to install libvdpau-va-gl1 and mesa-vdpau-drivers but at least for the latter, it told me that I already had a more recent version.
As I said before, I can live without the hardware acceleration for the moment, but that would still be a plus for some videos that my CPU pain to decode, so if someone has a solution...
These are video system info in Kodi if it can help:
