Yes. Your counterexample is an example of the Ostrogorski paradox, and there is good evidence that this accounts for a significant portion of why Democrats and Republicans fare similarly in elections despite the Democratic platform being more popular than the Republican platform on most issues.

The ranked voting method you're considering here isn't Ranked Choice Voting (RCV), it's Borda Count

• Borda Count works exactly as you say RCV works: The candidate ranked first gets 3 points, the second-ranked candidate gets two points, etc. This method is highly susceptible to strategic voting (voters can help out their preferred candidate by ranking D second instead of voting honestly) and parties can benefit enormously from running "clone" candidates.
• RCV (more precisely known as Instant Runoff Voting) works as follows: Tabulation proceeds in rounds. At the start of tabulation, each ballot counts as a vote for the candidate ranked #1 on it. In each round, if a candidate has more votes than all the other candidates put together, that candidate is elected; otherwise, the candidate with the fewest votes is eliminated and their votes are transferred to the highest remaining choices on their supporters' ballots (if possible). RCV is vulnerable to the center squeeze, so in your example it will fail to elect a pro-abortion, anti-immigration candidate.

I think what what you're looking for is a Condorcet method; they are guaranteed to elect a "beat-all" winner if one exists and do not have the extreme strategic issues of Borda Count.

Party list methods can be thought of as such, though I suspect that's not what you meant. Aside from party list, I don't recall any voting methods in which voters vote on sets of candidates rather than on individual candidates being discussed. Obviously you could consider all subsets of candidates containing the appropriate number of winners and have voters vote on these subsets using a single-winner voting method, but this approach has numerous issues.

You have to be careful with this argument because it's valid for any candidate-based proportional voting method. All such voting methods rely on the influence of voters who strongly support candidates who get elected being reduced with regard to other candidates, so all of them have such an incentive. (It takes different forms in different voting methods; in STV the incentive isn't to forgo ranking such a candidate altogether, it's to rank such a candidate second or third.) This does not mean the incentive for free-riding is equally strong under all candidate-based proportional voting methods, however, and I do think that strategy is more important under SPAV than under some forms of STV.

This is not a proportional voting method.

First issue: Suppose there are two opposing factions, one comprising 55% of voters and the other 45%, in a three-winner election. The smaller faction fields only one candidate. Let's suppose the 45% of voters marking this candidate as "good" is enough to get her into the top 3. Then this candidate has the most "bad" ratings and is permanently eliminated, leaving the smaller faction without representation. This issue can be addressed by not having the rejected candidate permanently eliminated.

Second issue: Suppose the same factions for a three-winner election, but suppose each faction fields many candidates. In the first round, three candidates from the larger faction have the most "good" ratings. Suppose the vast majority of voters in the smaller faction gave each of these candidates a "bad" rating and a bit over 45% of voters (who are in the larger faction) gave the elected candidate a "good" rating. For the next round, voters in the majority faction and those in the minority faction will have lost roughly the same amount of ballot weight. This again allows the majority faction to win all three seats. To fix this issue you'd have to have ballot weigh only depend on support for candidates who were elected.

With both of these changes, I think you'd be left with something that at least comes close to being proportional, though you'd still have some issues. It would be possible for a majority faction to prevent any one candidate from being elected by marking that candidate as the only "bad" candidate and by having hardly anyone mark a candidate as "good". (This strategy is terrible in practice and can be countered by having the minority faction run a "clone" of this candidate, but it still makes the voting method fall short of proportionality.)

(Disclosure: Vanessa is my wife.)

I want to share my thoughts on how the LTA can have a large impact. I think the main plan - to understand agency and intelligence fully enough to construct a provably aligned AI (perhaps modulo a few reasonable assumptions about the real world) - is a good plan. It’s how a competent civilization would go about solving the alignment problem, and a non-negligible chunk of the expected impact of the LTA comes from it working about as planned. But there are also plenty of other, less glamorous ways for it to make a big difference as well.

The LTA gives us tools to think about AI better. Even without the greater edifice of LTA and without a concentrated effort to complete the LTA and build an aligned AI in accordance with it, it can yield insights that help other alignment researchers. The LTA can identify possible problems that need to be solved and currently-unknown pitfalls that could make an AI unsafe (along the lines of the problem of privilege and acausal attack). It can also produce “tools” for solving certain aspects of the alignment problem that could be applied in an ad-hoc manner (such as the individual components of PSI). While this is decidedly inferior to creating a provably aligned AI, it is also far more likely to happen.

As for PSI, I think it’s a promising plan for creating an aligned AI in and of itself; it doesn’t appear to require greatly reduced capabilities and gives the AI an unhackable pointer to human values. But its main significance is as a proof of concept: the LTA has delivered this alignment proposal, and the LTA isn’t even close to being finished. My best guess is that, given enough time, some variant of PSI could be created as a provably aligned AI (modulo assumptions about human psychology, etc.). But I also expect better ideas in the future. PSI demonstrates that considering the fundamental questions of agency can lead to novel and elegant solutions to the alignment problem. Before Vanessa came up with PSI, I thought the main value of her research lay in solving weird-sounding problems (like acausal attack) that originally sounded more like an AI being stupid than like the AI being misaligned. PSI shows that the LTA is much, much more than this.