Safari’s Export as PDF feature seems to work every time for me. Not sure why I didn’t try it before, and just kept clipping webpages multiple times with the DT extension.
I opened a webpage, used File > Export as PDF, and saved it to the Inbox folder that imports into DT; PDF saved, and imported into DT as expected (yes, I checked the PDF for content).
Just for fun, I tried the same webpage with the Clip to DEVONthink extension, but things didn’t go so well, resulting in DT clipping a .webloc file instead of a PDF. I then tried using the clipping extension a second time, and DT correctly clipped and imported the page as a PDF (expected behavior, it always works the second time, but having to clip twice is kind of annoying).