The answer depends on what you want to do, which is information we do not have in your posting.
If you want your clipping to have the same formatting as the original clipping from the web, including images, fonts, etc., then use Rich Text, or Webarchive.
If you are only looking for the text and do not care about preserving formatting then use Plain Text.
If you are clipping from the web with the intent of later adding additional notes and comments to whatever you clipped from the web then use Rich Text (if you want to preserve formatting) or Plain Text (if formatting doesn’t matter to you)
If you want to append a series of clippings into a single file then use the Append Rich Note or Append Plain Note services.
I can think of no reason to clip as Formatted Note other than “because I can”. In my experience, clipping websites as Formatted Notes results in bizarrely mis-formed documents that are useless for most purposes.
Webarchive clippings are “completely local”, usually, but if the web page contains dynamic content (e.g., advertising content that changes) then it possibly can get overwritten. I find it better to convert Webarchives to PDF if I’m interested in preserving the content.
All of the above is dependent on the web site you clip from. Some sites make gobbledegook Webarchives. Other sites won’t let you clip much or at all if there is a strong paywall or other behind the scenes trickery going on. YMMV and usually DEVONthink can do nothing about misbehaving web sites.
Not necessarily. It depends on what content is being delivered dynamically. The entire article, text included, could be served from another domain. This general behavior is very prevalent on many monetized and click-bait style sites, including many popular ones. (I’ll bite my tongue on naming names )
They are related. RTFD is “Rich Text Formatted Directory”. It is a “package” — a folder that macOS makes appear as a single file. Inside that package folder is the text file (an RTF) and whatever images need to appear in the text file when it is viewed. If you clip text + images you will get RTFDs. If you clip text only you will get RTF. The difference, simply, is the presence of images in RTFDs.