I mostly agree with everything you have said and I think that this would be a great way for a lot of bots to work.
That being said, I do have a few reservations. Firstly, unlike with humans, it is difficult for users to reply to a bot if they require further information, so this would have to be taken into account. Secondly, this could result in a large amount of email spam.
Also, bear in mind that currently the bots on ForoTree only go through profiles on a user's watchlist. That means that primarily the user who will first see the alert will be the user who activated the bot. If this user then goes through and makes all the changes manually, surely it would make sense for the bot to just go ahead and make the change? Obviously it will depend on the change.
There are also some general exceptions where this makes the bot altogether useless, although I appreciate if you don't agree with the use of such bots.
For example, one of the bots that is currently being tested on ForoTree is the "Family Search Citation Cleaner". The purpose of this bot is that when a user cites Family Search they can just copy and paste the citation from Family Search into an inline reference and then leave the profile alone. The bot then goes into the profile and tidies it up so that when that person or someone else goes back into that profile later, it is much easier to edit because the bulk of the citation has been moved to the bottom of the page.
Now I understand there are various different methods of doing this and that there are ongoing discussions about these various methods, and that debate will continue elsewhere.
However, regardless of the particular method adopted, my point with this example is that the whole purpose of this particular bot is to save the profile manager time from having to tidy up source formatting. If this is the primary aim of the bot, then posting a comment to let the profile manager know that their sources need tidying up is not going to be helpful at all. In fact, it would probably be more of a nuisance.
If you haven't already, I would recommend taking a look at Wikipedia's Bot Policy to see how it is managed there: