"Handling" dependencies automatically is fantastic when it works. But it reaches varying degrees of anarchy and hopelessness when it doesn't.

The more ambitious the framework, the more you have to wade through to figure out what it's actually doing when something breaks...I'd much rather have to deal with some cross-compilation headaches and dependencies than to be at a dead end when the 'black magic' stops working.

Or, I assume, when the company behind the service goes out of business or shifts focus...

That is a risk when you use any service, even if it is open source.

What kind of dependencies are we talking about? Compiler, BSP, peripherals?

Libraries, mostly:

https://platformio.org/lib

And yes, it handles compilation/flashing/etc automatically.