I use Devonthink mostly for archiving websites. But there is one big problem: When save the content as html or web archive or PDF and later look at the saved pages in Devonthink, there is very often a big pop-up (often for Cookies etc.) in the middle of the page and hides the whole content. Saving as a bookmark is not good enough for me and saving as html works as I can dismiss the pop-up most of the time when I open the page in Devonthin later, but then the pages reloads each time that I open it in devonthink and I want to have a static page. Evernote has not problem to save the webpages without the annoying pop-ups.
I’m saving web pages as PDF to get static content all the time and the experience has never been consistently good. Not only with DEVONthink but with all apps. All web pages behave differently and because of that different approaches are needed to get the best results.
When clipping with the browser extension does not work as expected
Print/Save PDF to DEVONthink 3 is often a valid alternative. As printing does respect if Reader View is on or off it is worth trying both.
With the web clipper clutter free mode in my experience is the most reliable option but it works best with mainly text content.
I always use the clutter free mode, but it doesn’t help with the popups. Saving via the print menu is too tedious, its much faster and easier with the DT menu button. I like that DTs webscraper is really fast, much faster than Evernote, but the popup issue is annoying.
If you set a keyboard shortcut in system prefs for the Devon print service (I use cmd+P), you can achieve clipping in 2 shortcuts (cmd+P, cmd+P), just like you would need 2 shortcuts or 2 clicks to invoke and save from the DT clipping menu. It’s faster with the printing option in fact, because there is no network traffic involved, just import.
Also mentioned here: