I agree with you, but I will say that Markdown (or at least, all the major "standards" for it) support interleaving HTML both inline and at the block level. Unless you are writing a very bombastic document or want to avoid a rendering step, I'd argue that you'd be best served by just writing CommonMark with embedded HTML.

I'd argue that, at that point, you might as well write HTML. I find it easier to work with one format at a time rather than two intermixed and a typical Markdown document is barely more readable than its equivalent HTML document, while the latter gives you a lot more flexibility and semantic accuracy.

versus markdown it is ungreppable with all the escape codes/entities, then you have to use special tooling for search.

Avoid character entities—store your HTML files as UTF-8 and just embed everything.

I guess that mostly works but lots of my notes have <>'s. I guess <code> covers most of that