It seems like you have done some attempts of trying to reduce the negative impact by asking for which tools the Community uses. However, there are many other small user scripts and applications that are probably only used by a few people and not worth considering on their own. Community user scripts and other apps have all sorts of reasons (including but not limited to moderation) to access various pages. I guess most access to question/answer pages can use the API but this isn't the case for more niche-things.
That being said,
What stops you from limiting these restrictions to question/answer and similar pages?
From your post (and other posts in the past), it seems like the main problem you are dealing it is scraping the user content you are hosting (if it isn't, correctlycorrect me and tell us what else you want to achieve with this). If you want to block this, you could do that by implementing these restrictions on question/answer pages, maybe the search and a few other pages you don't want people to scrape. This would mean most Community applications and user scripts that don't request many additional question/answer (and similar) should be unaffected.
Please only restrict the sites you really want to restrict. There isn't much reason to limit automated access to other site and it is doing unnecessary damage.