However, having used the tool for more than a year at a 20 person org, one of the biggest pain points I have seen is people not knowing where to place new pages. There is "Notion anxiety" about not wanting to mess up the board.
One thing we've done to address this is by adding two common tables, the Documentation table and the Meetings table. Anytime anyone wants to create a new doc, they can simply add it to the documentation table and then tag it to their team, and we have a full list of all of the docs everyone has written. From there, if a certain piece of documentation needs to be somewhat else, it can be pulled out and moved there. Additionally, each team member has a default "project board table" and if you say need to create a quick to do list, you should just add it to your personal board. Having these "default tables" rather than a special table for each specific project may really help your team.
Notion requires intentional planning, and you need to be opinionated about the architecture. If you just keep adding things on haphazardly, it's going to turn into a mess.
Finally, I do agree with OP that notifications could signicantly be improved. If anyone from Notion is reading this, please think of notifications like emails. At the moment, notifications are only in the state of read/unread, and as soon as I open my notifications, they clear. Instead, I want my notifications to be a mini-inbox, where I can view notifications, respond to notifications, archive completed notifications, and filter notifications into channels (the same way I can filter emails). Notifications are a to do list, and should be thought of as such. Having this set up would address OPs concern about being able to filter notifications at the email level by setting the filtering logic in the app.