"Placing" linked PDF File in Illustrator for Markup Edits?

Question

When I highlight text in a PDF file that is linked to an Illustrator file (PDF is "Placed" in the Illustrator file as a linked object), text highlights in the PDF file do not show up in Illustrator when I update the link.  Does anybody know why, or is there some setting or workaround to force the PDF markups to show up in Illustrator?
Reason for Question
I often use Illustrator as a PDF editor because it is much more flexible than Acrobat's clunky editing tools.  There are some significant problems however.  If you open a PDF page in Illustrator, you lose some stuff like paragraph formatting, which Illustrator wants to left justify (same problem when opening an AutoCAD file in Illustrator).  You can also have trouble with missing fonts like Helvetica, which isn't a default system font because it is licensed and expensive.  Illustrator will swap the missing font out with a substitute so it can edit the text.  (Acrobat will do the same thing if you try to edit a font that isn't loaded in your system).
A workaround to maintain exact registration if I just want to mark up a PDF file (rather than changing the text) is to "Place" the PDF file in Illustrator.  When Placed, the file behaves like an object the isn't editable in Illustrator (you can edit a Placed object from Illustrator, but Illustrator will use the authoring application to do the edits, in this case, Acrobat).  I you are interested doing the same thing,... when I use Illustrator to mark up another file like PSD, JPG or PDF, I initially open the file in Illustrator to capture the dimensions, and then delete everything, and then "Place" the file back into Illustrator.  You can optionally link or embed the Placed object.  After Placing, I use the transform tool to move the Placed Object's upper left corner to 0,0 (XY Coordinates) to acquire registration, lock the layer, and do my markups on separate layers.
This procedure is a bit clunky and requires multiple construction files but Illustrator's vector tools are much better than the most of the markup tools (but not all) in Photoshop or Acrobat.  A Photoshop file will link to Illustrator, and you can export it back to Photoshop, but the Illustrator construction file will not be "linked" into Photoshop, so if you need to make changes with Illustrator you have a couple of options.  You can open the Illustrator smart object from Photoshop (Photoshop will launch Illustrator to do the edits), or you can delete the smart object and work on the Illustrator construction file directly and re-import.
Since you can't select the text of a Placed PDF file object in Illustrator to highlight text, I'd like to do some of the text highlighting in the linked Acrobat file upstream of Illustrator.  I should be able to bounce back and forth with both files open, the Illustrator construction file and the linked PDF file.  Problem is that when I add a highlight to the PDF file, it does not show up in the Illustrator placed object that is linked to the PDF file.
So back to my original question.  Does anybody know why PDF text highlights do not show up in Illustrator when the PDF file is placed as an object in Illustrator?  Is there a workaround to force the PDF text highlights to display in Illustrator?
FYI, I working on a business presentation and need to mark up a few pages of IRS publication 463, which is a 58 page PDF document with a bunch of "destination" links (10 to 20 links per page).  I can extract a page, do my markup edits, and then "replace" the page back into the original Acrobat file and all the links and bookmarks will still work, but registration is critical.
I'm using CS6
Thanks in advance for your insight.

Answer 1

Mylenium, Thank you for your on-point explanation of why the markups don't import into Illustrator.  Based on your input, I did some digging and discovered:
I can export the Acrobat "Comments" (text highlights, but not markups?) to a FDF file
http://help.adobe.com/en_US/acrobat/pro/using/WS40A4853E-0D48-46a6-8AB6-6B9A27A22D83.html
and then optionally re-import them to another PDF, including a blank document (with the same dimensions to maintain registration) or the final output file.  I can then open the PDF (that contains the comments only) using Photoshop and save as a PSD file.  Photoshop captures the text highlight color graphic without the white background or text so I am able to achieve transparency.  I can then "Place" the Photoshop file as an object on its own layer in the Illustrator construction file as either an embed object or a linked object, but I tend to link for a number of workflow reasons.
Quite clunky, but it seems to maintain exact registration (although for some reason, whenever I place an object in either Illustrator or Photoshop I need to move (transform) the object corner to 0,0 because it is typically off by a pixel or 2).  Not sure if there is a way to also export PDF "Markups", but my objective was to use Acrobat's highlighting tools combined with Illustrator's vector graphic tools for markups, so even if I can only export the Acrobat text highlights and not the "Markups", I can still achieve my objective.
From a work flow perspective, I may optionally choose to use the text highlights only as a reference in the Illustrator construction file and turn them off when saving back to PDF.  I would then import the text highlights (FDF file) into the final PDF so they are actual Acrobat highlights rather than raster objects, but I do have the option.
I have also noted that I can print an Acrobat file to PDF to capture the text highlights, but that method introduces problems with registration and transparency (the white paper background).  I'll often print my final output to PDF rather than saving to achieve a small flat file that will render consistently on different computers, but in this case registration is important so it is better to save to PDF and live with the larger files size.
Why all the fuss?  Acrobat is good at highlighting text and Illustrator is good at drawing stuff like curvy paths with variable strokes.  Illustrator also has layers and stacking order control.  (Acrobat has clunky wannabe layers that are good for limited stuff like multiple versions, but not much help with graphic composition or stacking order).  I need workflows that can merge tools from multiple programs (Acrobat, Photoshop, Illustrator, Autocad, and Solidworks).  I could do my vector markups in Illustrator, then save to PDF and do the highlights in the final Acrobat file, but if I need to change the vector graphics later I would lose the highlights.  Doing the highlights in a separate PDF file and then exporting to a FDF file lets me make changes in Illustrator without having to recreate the highlights from scratch.
Thank you for your assistance.  If you have any additional suggestions I am always striving to improve my workflows.  btw, I've experimented with some of the 3rd party PDF editor's, but not the expensive ones (less than a few hundred dollars).  Most of them do a few things better than Acrobat, but they all have their shortcomings and I'm leery of investing my time in applications that might be obsolete in few years.  Perhaps this discussion is better suited to the Acrobat Forum, but I do a lot of PDF editing with Illustrator despite its limitations.