I had a similar problem. I too wanted a link in an embedded page to point to a bookmark in the containing page. But I am not sure if our circumstances are exactly the same.
A local link such as
<a href="#BOOKMARK">
will only look for an anchor in the same page as the link, i.e. in the embedded page. An approach such as
<a href="containing-page.html#BOOKMARK" target="top">
will only work if your link always references the same containing page. (The target needs to be specified, to display the page outside the iframe.) I am not sure if this will meet your needs.
If you want to re-use a common bookmark name in different containing pages, as I do, the design effectively requires the destination url to be treated as a variable, and that cannot be done using pure HTML. It requires javascript or similar.
It was in fact more elegant for me to add the bookmark link to the containing page, so that I do not need to standardize my bookmark names. This does not even need javascript, just a bit of css.
What I did was to position the bookmark link over the embedded display, so that it looks like it is part of the embedded page. In this example, the iframe is fixed at the top of the page and the bookmark link positioned over its top left corner.
<iframe style="position:fixed; left:0pt; top:0pt;" src="embedded-page.html"></iframe>
<div style="position:fixed; left:0pt; top:0pt;">
<a href="#BOOKMARK">My Bookmark</a>
</div>
With a bit of css refinement, this gives some flexibility of layout. For your issue, you may need to stick with javascript.