Well, now we have an even better answer to this earlier question:
Because we don’t have a choice: nothing will make DEVONthink detect changes made to the file attribute underlying the URL field, and thus when using an external application, the only way to add a URL to a file indexed by DEVONthink is to do it indirectly (in this case, by first writing the URL as a Finder comment and then duplicating it to the URL field).
That’s right and that’s why the Finder comment should actually be sufficient for the current workflow. Changes of the comment are detected and according to A new tool for Zotero users a smart rule copies the comment to the URL field. But probably I’m missing something important 
I may be getting confused about something. When asking about why the redundant info is needed, are you talking about the duplication we’re doing in DEVONthink (i.e., the part about copying from the Finder comment to the URL field)? Or are you wondering about why one would use an external tool to write in both the Finder comment and the URL field simultaneously?
About this. According to your description I guess that the Finder comment plus a smart rule should be sufficient.
Ah, okay. I’m sorry if there was confusion about this – this is not what I’m doing (and I don’t think others are doing) and not needed for the current scheme. It is possible to write both simultaneously with Zowie (instead of one or the other), but as you noted, there’s no need.
The reason I went down the rabbit hole of dealing with the wherefroms field is that if DEVONthink detected changes to the attribute value and used it for the URL, then there would be no need to the roundabout approach of first writing the Finder comment and then using a smart rule to update the URL. People could write Zotero select links directly to the wherefroms metadata field, and that alone would be enough – no smart rules or other copying needed. (Avoiding the need for a smart rule would be beneficial, because of timing issues involving interaction with Zotero.)
It would not be necessary to write to both the Finder comment and the wherefroms in either scenario.
An update for anyone coming to this thread: I’ve released a new version of Zowie that has a new option (-s or --space on the command line) which makes it write the Finder comments with a trailing space in the text. This is a hack, I know, but it has the effect of making the Finder comment and the URL in DEVONthink sufficiently different from each other that DEVONthink will no longer ignore the Finder comment, when the comment is copied to the URL field by the typical smart rule approach. I find the result less confusing, and others may too, but the option is off by default and has to be turned on deliberately.
As an aside, I’ve also developed some better ways of producing runnable self-contained single-file applications from Python programs. The new release of Zowie now comes with binaries for all versions of macOS.
Downloaded the new version, ran it with the -s and -o flags on my entire library and now it’s all nice and clean. Thanks for figuring that out!
Glad to hear it worked! Thanks for letting me know.
@cgrunenberg One last question related to this topic. I was reviewing my smart rule for copying the URL from the Finder comment to the URL field in DEVONthink, and at some point in the past I used “every minute” as the “perform the action” triggering event. I now wonder if there is a more efficient way to trigger the rule. Will any other event be generated if an external application changes the Finder comment on a file indexed by DEVONthink?
No, that doesn’t cause any smart rule events and therefore a scheduled smart rule is still necessary.