While that is understandable, it's something which is clearly causing an issue, and refs need to ref the game as if there is no VAR. I assume they're being instructed to do that.
I still don't think it should have been a penalty anyway.
I actually don't think our onfield refs are that bad. It's a really difficult job and I doubt I could do it as well as them even if I had a lot of training. But there are two issues where I would be better. I wouldn't put up with the 'us against the world' attitude they seem to have, and I think...
So if MOTD were running VAR, they wouldn't have given the penalty, because it's not VAR's job to overturn a subjective decision.
It would have worked if anyone with a brain was in charge of it. So it can be fixed.
They could run a training session with the refs - if they got them all together...
But 'it kind of is nowadays' is not a clear and obvious error that needs overturning. That's the issue here. If the ref had given it I'd have felt unlucky and that it was soft, but he didn't. Overturning his decision was just plain wrong.