I'm not sure I see the actual problem. I understand you are talking about the "Tags blacklist" text field, under the "E621 search" option, which is filled on first start with the e6 default blacklisted tags.
But it only contains 8 tags, and upon changing it, the changes will be saved to the browser's local storage, so it remains the same next time you open the webpage.
As you describe your problem, I'd assume you'd go through each of the 8 default tags and erase whichever you don't want filtered out, and that would be a one time issue since this blacklisted tags change will be saved once you start the game.
If you say you "don't have the issue" on the APK version, your browser settings are likely set so data isn't allowed to be saved, and you'd probably also lose all your saved lists data (which can be exported/imported however, so that could still work out I guess).