I’m not an expert on Duke specifically. But what I have gathered from listening to AOs at a variety of highly selective colleges discuss grades and transcripts is they are primarily interested in the grades for courses you took for HS credit and that appear on your HS transcript.
This makes sense to me because ultimately they are trying to come up with comparable internal academic ratings for different applicants, and it is already incredibly complicated just to try to “normalize” different HS transcripts. They are often putting a lot of work into doing that, including possibly with software that helps them process transcripts, possibly fold in other contextual information, and so on.
Adding in other courses not taken for HS credit would require even more complex analysis, and yet would only be relevant for applicants who do that. So it makes sense to me they would typically not want to further complicate this already very complex task in this way.
In addition, one might suggest putting much weight on such courses would potentially be problematic because while generally speaking kids in the US have free high schools available to them, additional classes not for HS credit can be quite expensive. And I gather colleges often prefer to treat expensive academic programs outside of HS more as demonstrations of interests versus actual qualifications for this reason, among others.
In any event, you have done what you have done and you can see what happens. I again would just suggest you have modest expectations.
Of course that is up to you. But there are so many other private research universities and LACs that would at least provide a very different experience from UCR/UCM. Given that you seem interested in that sort of experience, to me it would make sense to look at those alternatives too. But again, if you are confident you would rather attend UCR/UCM than those other sorts of colleges, unless US News gave them a ranking at that level, then that is up to you.