For now, I've solved this to my satisfaction.
Dragging and dropping an HTM/HTML file into Calibre still puts the "Go To Beginning" at the first Table of Contents entry. So, since I use H3 and H4 tags for Chapter/Sub-Chapter TOC entries, I add this line at the beginning of every HTM/HTML <body> section:
<div style="visibility: hidden"><h3>Title Page</h3></div>
This makes a TOC entry called "Title Page", and starts the book there, but the words "Title Page" don't show up in the text.
I'm happy enough with that, and having the "Title Page" in the TOC is ok. I really don't want to modify the opf files manually, and would prefer that Calibre did it for me automatically with the old <a name="start" />.