Let's see...
You're perfectly willing to let RH display HTML code in your
project in WYSIWYG mode, keep track of all your topics, images,
etc., generate an online triple-frame output with TOC, Index,
Search, and Glossary, as well as a print version, prepare online
output for multiple browsers that refuse to display some forms of
code that the other browsers do, yada, yada, yada.
However, you balk at its methods, that is, adding some
specific code for its own purposes.
We are all RH users, here, with challenging jobs of our own.
We have all worked with multiple versions of RH (some since the
early 90's) and other HATs (some since the late 80's), and we have
mostly learned to deal with HATs as we would with crazy Uncle
Harry. And that is, to accomodate his quirky behavior as necessary
to get through Thanksgiving dinner.
Good luck,
Leon