You have hit the nail on the head in terms of what I think is the biggest bugbear with VAR. It seems the VAR overlords have the final say.
I do not know the exact answer to your question - but we have yet to see an example of where the ref seemingly has had the final say (But then we dont know as there is no 'public' nature of information flow between VAR and the referee.
I think the biggest improvement to VAR would be, for everything bar the bleedingly obvious incorrect decisions that can be quickly fixed or offsides (Where they have gone down the route of trying to do micro-precision analysis), that the on field referee remains the decision maker. VAR can review and tell him he must go and look at the screen and reconsider his decision, but he remains the ultimate decision maker. He (or she one day perhaps) must then be willing to front up and explain his decisions after the game, if it disagrees with the footage. Add to that a requirement that wherever possible replays are shown at the ground as they are watched for VAR (noting the pond in Trafford and Klanfield need to get with the times), and that the conversation is streamed live (As it is in rugby union and rugby league) so everyone knows whats going on, and a lot of the issues with VAR will go away.
But that would encourage transparency and remove the ability for VAR to potentially drive an agenda (not saying it is being used like that at the moment) - and that seems to be what I suspect many think is the real driving force behind the half arsed way it has been implemented this season.
I reckon had the referee had the final call yesterday, it would have stood as a penalty. On the basis I think he adjudged it to be accidental handball, but the body being 'unnaturally bigger' as per the rule. I don't think anyone can mount a strong argument that such a conclusion, when made live as it was by him, by necessarily unreasonable - certainly not a 'clear and obvious error' as VAR rules are supposed to stipulate. Its very noticeable in their press release/dribble about the decision that they seemed to solely focus on the aspect of 'boot to hand', but conveniently ignore the other aspect of the rule (I.e. the body must also not be naturally bigger). Very selectively presented to try and suggest a 'clear and obvious error', when I'm not convinced there actually was one.
I wish the referees were made to justify their decisions, or at least be able to be asked about them. But for that to transpire, it will need a complete shift on what VAR is and how its implemented.