I'm currently using scrapbook for Firefox and it's great for saving pages but not to add my own notes and annotations to it. Either the tools have the same restriction in features or they are doing very bad in saving an offline HTML page.

Have a look at RightNote. You can even import your present scrapbook data.

I'm pretty happy with AML Pages for this purpose

I use Microsoft OneNote for web clipping. Lets me clip the whole page, portion of the page or just the article. Easy to add notes.

This might be of interest:
Re: Transform list of url links -> copies of actual web pages - try WebPageDump?https://www.donationcoder.com/forum/index.php?topic=42424.msg397021#msg397021

The above post refers to Zotero (standalone app and Firefox add-on) and the Firefox add-on Scrapbook as providing the best webpage copying (by far), and how they both use the same engine - WebPageDump.

I also use OneNote (Office 2016) very heavily and rely on it as my primary PIM and "21st-Century Zettelkasten", but copying webpages is not one of its fortés, sad to say.

Voilà (OS X) will capture the active URL from a browser and create a full page image of that page -- everything including the portions that are have scrolled off the top or bottom. The capture can be dragged out of Voilà as PDF or other image formats, for annotation or whatever.

The Wagbee beta is coming along nicely, excellent for trimming the actual gems from pages and putting into a timeline context.

RightNote is awfully hard to beat for simplicity and accuracy in saving a webpage as a note. There are other programs where saving webpages is the main focus, but integrated into a full outliner/tree-based organizer, RightNote does an excellent job.