It's true that the flag is setting some particular context that becomes difficult to ignore afterwards. The choice of using a flag was meant to discourage the type of vote brigading that we find on Reddit. The Bitcoin blocksize debate with wars between /r/btc and /r/bitcoin where opposing views were systematically downvoted into oblivion participated to the creation of echo chambers. We want to avoid this kind of thing happening here, but we may not have to do anything to prevent it because of the economic incentive stake holders have to ensure that the platform remains an enjoyable and user friendly space, which implies that downvoting should be done wisely.
I never used Reddit and wasn't privy to the Bitcoin block size debate, yet I follow. I appreciate the explanation. Down voting has a cost.
However some users will not be motivated by pure economics.
This is true. The assumption is that a user who holds a lot of stake is likely to have either invested (which normally implies some level of understanding of long term economic incentives) or received the stake as a reward for posting good content or curating (which implies that the user is relatively constructive, intelligent, sociable and not a complete troll). Although this isn't exact science and there will certainly be many stakeholders who will use downvoting unwisely in spite of the fact it reflects negatively on their investment. But it is expected (hoped?) that such stakeholders will not be collectively holding a large amount of stake.