MongoDB made an explicit exception to AGPL. Normally a driver wrapping an AGPL database would have to be AGPL too. In turn every app using the driver would be AGPL. But Mongo, as owners of the driver and DB, made an exception for users.
The only situation where AGPL wouldn't affect other components is where you're using industry wide standard APIs. E.g., I can use Firefox to connect to an AGPL website, but that doesn't make Firefox AGPL. This is what Stallman is getting at when he talks about intimacy of API communication. He points to a simple call to main as an example that's not intimate communication and thus has no licensing consequences.
Also you can't say "we license this as AGPL for non-commercial use". That violates the rights of the user to not have additional restrictions placed on the AGPL. And if you think through the practicalities of how that would work, it's not feasible anyhow.
Edit to add: AGPL does not prevent private modification of code. Your are required to license the code as AGPL and distribute the AGPL licensed project to users, but if the user is just you, there's no practical effect. However, once you start sharing it internally in a company, it's a giant grey area especially if you have contractors or any non-employee ever access your infrastructure. Employees might also be able to claim they are entitled to an AGPL copy of it. The only thing that's allowed internally is having someone "make modifications exclusively for you, or provide you with facilities for running those works", which would be effective for a trial or POC. Essentially you should either plan to abide by the AGPL or plan on buying the dual license at some point (the license allows violations to be fixed within 30 days).
(This post is for entertainment purposes. I am not a lawayer, and this is not advice.)