Zooming and shrinking the annotation itself can certainly be done - and indeed should be. For both PDFs and EPUBs.

Having the margins as a special mark-up zone partially helps solve the "what was marked up" problem as long you'll accept that the markup appears approxmiately where you put it.

For example, if you had the line:

AAA BBB CCC DDD EEE

and you wrote in the margin to the right of "EEE" something like "What does this word mean" (where you knew you were referring to "EEE"), then the software, at best, could ensure that "What does this word mean" appears in the right margin, either centered or positioned relatively to the line as you originally wrote it, on the line where "AAA BBB CCC DDD EEE" appeared. Note that the software cannot know what word you were "annotating". Was it "AAA"? Was it "CCC". Only you know it was "EEE". The line "AAA BBB CCC DDD EEE" does not have an internal line number that the software can use. It would have to choose one of the words, or record that at the time of the annotation the (nearest, centrally located) line started with the word "AAA" and ended with the word "EEE".

Now, you change the zoom. now you have the lines:

AAA BBB CCC DDD
EEE

or, "worse", it splits across a page:

AAA BBB CCC DDD
----page break ----
EEE

Now - does the annotation belong beside the first line, or the second line? You were annotating "EEE" as far as you were concerned, but the software doesn't know that.

The page break adds another problem, too. The first line is at the very bottom of the page, and the second line at the very top of the page. If you had written a long annotation (say one that spanned several lines vertically), now the software has to somehow decide how to position the annotation. That will work, maybe, if you were writing words.

But what if you instead drew a "}" or "]" type of mark? And what if that vertical line-type squiggle originally spanned mutliple lines and now you have a page break in the middle. Does the software render your vertical squiggle, which you meant to denote a range of text, on the first page, or the second page, or both?

Zooming the squiggle to match the text zoom is easily done (I should hope Adobe/enTourage can manage that part), but what about where the squiggle gets positioned?

You see, it's the "edge" cases that are the problem with markup annotations in EPUBs. A squiggle in the middle of the page in the right margin is an "easy" case.