What kind of mod tools do the apps allow that Reddit does not?
I do not know if these are mod tools I would agree are necessary (e.g. bans for repeated spam) or are these tools that I would agree allow mods to abuse their power (e.g. ban users are who mere followers of other subreddits).
Frankly, I fear unofficial mod tools could lead to much worse problems if at least portions of the API are not carefully rate limited. Here I include pricing as a type of rate limiting and this could be Reddit's attempt at reeling in this abuse (even if only for IPO reasons). A particular egregious example of such an abuse would be to download all new users' history of posts to make a race determination and ban a new user because of that. Sure, a mod could do this manually using Reddit's UI, but it would remain more difficult to automate this on a large-scale.
There is absolutely no way they are not aware of this.
No, they've made a conscious decision that completely alienating and driving away the parts of the communities which care about all of this stuff is a price they're willing to pay.
It seems pretty clear that they believe the people who will leave are not crucial enough (in function and number) to make the overall communities collapse, and that the result they want to achieve is worth the losses.