The problem is real
I have some personal sentiment for this issue, as I got out from between this rock and hard place myself not too long ago.
Keep in mind that there are many users that are high rep on many sites, not just one. I'm above 1000 rep on four communities and above 500 on an additional six. That means I'm trusted on ten communities to downvote appropriately. If that's not a decent representation of the SE network I don't know what would be.
Here's the problem with this pickle. Even with an association bonus, you have to post if you want to gain the downvote privilege. I suppose you could edit, but that seems a strange way to earn rep in any decent amount or timeframe.
Now you come in to MSE to check out a post that says the whole network will be affected with some proposal. You don't like, and you probably have decent reasons. But you can't vote on it! You're trusted on more than 10 other communities across the network to downvote, but somehow you're considered not trusted here.
Your only recourse is to make an answer saying you don't like the idea and list a few reasons. But if it happens to be an unpopular idea, your answer will be downvoted, making your situation even worse. So now you're annoyed and don't even want to bother next time. You're at a point where you don't even want to suggest anything because it may be downvoted, hurting your chances to have an equal opinion even further. This reinforces the already skewed opinion and disenfranchises new MSE but SE experienced users from participating.
And if you're clever enough, you just find a niche in this cronyism and exploit it. In other words, you make duplicitous posts that you don't necessarily agree with just so you can earn the rep to have the luxury of being honest in the future.
Ideas to fix it
I think it is clear that the current system is not as good as it should be. I'm not sure how to make it better, but in the case of already being trusted with the downvote privilege on multiple SE sites it makes little sense that those users cannot be trusted here.
I realize it would increase the complexity of the situation, but rep on MSE is useful and should certainly not be put away. The higher rep privileges like Mod tools, should distinctly belong to trusted users of this site, regardless of their trustworthiness on other sites. So adjusting the downvote privilege to a lower rep threshold does make some sense. In the least, it should be equal with the upvote privilege.
But a thrash of downvotes on MSE can be pretty harsh. It's hard to watch your rep take a 30+ hit just because you made one unpopular feature request, especially when you only have 101 rep in the first place. And getting 15 downvotes is not really that uncommon.
Again, I'm not sure the best way to fix this, but it is certainly entry prohibitive, even for seasoned SE users, who are really the people you want on here regularly, not those goons with 10K rep on MSE and only a nickle's worth everywhere else.