You are confusing a number of issues of the WebArchive file format, Web site design and dynamic graphical elements with supposed ‘bugs’ in DEVONthink and the Clip to DEVONthink Safari extension.
If you have the AdBlock extension enabled in Safari you may not have even realized that the MacRumors site is putting up a series of ads on the page, most of them with dynamic content.
Dynamic graphics create all sorts of glitches in WebArchive captures of a page. Some of those glitches involve displacement of the graphics or repeating presentations of a graphic. The resulting WebArchive will look awful. But that’s not DEVONthink’s fault.
An especially irritating feature of a WebArchive that contains a dynamic graphic is that when displayed, it will attempt to go to the source page and download the rest of the dynamic series. That’s not a bug in DEVONthink.
When you use Clip to DEVONthink to create a WebArchive of a page, the URL is passed to Apple’s WebKit and the page is re-downloaded and processing is provided to save the page in the chosen filetype. WebKit doesn’t include AdBlocker, so the ads are included – and those glitches will therefore result.
I usually don’t capture data from the Web as WebArchive. For one thing, it has been the least stable of any of Apple’s proprietary filetypes. It also takes considerably more storage space than a rich text capture of just the information that I wish to capture from the page. I’m interested in the content, and not the layout of the Web page or extraneous elements such as ads.
I do find WebArchive captures useful in some cases, such as when I want to capture a forum thread that includes scripts, which are included in scrollable boxes within posts.
In that case I’ll select just the portion of the page that I wish to capture and invoke the Capture as WebArchive Service, using the keyboard shortcut ‘Command-%’. This is an instant capture of the selected portion of the page as it is displayed in Safari. So if you had AdBlocker turned on and select the entire page for capture, the ads won’t be captured. You might see some other minor appearance glitches resulting from complex frames in the page design (that the Web page designer could probably have prevented with a bit of forethought). If dynamic images have been avoided in the selection of material for capture, the WebArchive won’t attempt to go out to the Web when opened.
Of course, a major payoff of capturing just the desired information content of a page to my database is that searches and See Also are not ‘confused’ by the text of extraneous content in the original Web page. I’ve got better information ‘focus’ as a result.
Re fonts and colors for RTF editing: The standard OS X tools are available. Press ‘Command-T’ to pop up the means of choosing fonts, sizes, colors, etc.