There have been proposals to more reliably know the value of automatically generated (heading) IDs and to be able to manually set (anchor) IDs, e.g. ## Example ##{#myidentifier}. In theory, you probably could use XLink for arbitrary link targets, but that would depend on the output format.
Could you please be more specific why you would want to indent blocks of text? Quotations with > line prefixes might be the answer.
There are some extensions that are using double equal signs to generate the <mark> element in HTML, but you would need another extension for adding attributes of you wanted different colors, resulting in something like foo ==example=={.red} bar.
You’ll find several (long) threads about (competing) formats for tables around here. Some are optimized for writing, some for human reading and some for machine parsing. Most of them have been implemented somewhere.
You can mix HTML with MD/CM. There are just some restrictions on the syntax of HTML to follow, which avoid ambiguous situations. Most of them many authors comply to anyway.