Or just monitor the stories that get flagged off the front page (~25 over several weeks according to the post) and take appropriate measures (e.g. restoring with relative time and penalize flaggers). Of course they first have to decide whether they want users who cares about the stories they submit and therefor think that non bad things getting flagged off the front page is a problem.

Then people would just submit clickbait titles such that their submission gets quick upvotes for flag immunity.

Good point -- but certainly you can agree that after a certain point threshold flagging is increasingly less valuable and should be more to simply let the mods know to take a look.

Anything is preferable, at this point, to the methods used. Perfectly good articles are getting dropped and it comes across as censorship.