You said :
"Time for this stupid rule to be rethought (like the whole offside rule for me)."
How would one "rethink it" with VAR remaining in place to get around this problem? What I am saying is that the problem is inherent to VAR.
Lets think it through. If they do away with the "linos keeping their flags down problem" then you "interfere" with a possible corrective "outcome" of a VAR review. If a lino puts his flag up and it turns out that it was in error, then there is no way that VAR could then "retify" the situation as in their minds the situation would need to have played out as it would have "just in case". Of course this way of thinking is antithetical to how football works, how it was designed, etc. But essentially they need for linos to keep their flags down to allow VAR to work, or in the way that they want it to work. If the linos get back to doing their job, all of a sudden VAR has a problem because then it can't correct errors in their minds and they have so much invested in everything that would effectively render VAR useless in that regard.
So while I wholly agree with your sentiment, the "stupid rule" as it were, or merely the inherent disruptive influence of how VAR needed it to be changed, for VAR to work, it essentially "broke" the rule as it was prior to VAR, which had been working just fine for generations.
So the idea of rethinking it again, from the same people who rethought it to begin with which got us to this point, is maybe a tad scary to think of how they, the people who broke it in the first place, might rethink it in trying to improve it.
I'm trying to remind you of the underlying conundrum in how this could be rethought while having VAR in place. But if you have any ideas please let us know. See the VARers mentality as it pretains to "continuity" is fundamentally diferent than ours, as in the fans. They think that disturbances to the flow are fine as long as the sequences between their interruptions can be pieced together like a jigsaw puzzle as it the match itself is a film in post processing.
I'm trying to hammer home that VAR is inherently hostile to the match and as long as this elephant remains in the room, on the football pitch, etc I don't see how this problem is remedied by further rethinking. But if you have any suggestions or ideas on how this could be effectively rethought within the VAR framework, or without, please let us know.