This is a good point, and one that we are taking into account when developing ty.
The benefit of the gradual guarantee is that it makes the onboarding process less fraught when you want to start (gradually) adding types to an untyped codebase. No one wants a wall of false positive errors when you first start invoking your type checker.
The downside is exactly what you point out. For this, we want to leverage that ty is part of a suite of tools that we're developing. One goal in developing ty is to create the infrastructure that would let ruff support multi-file and type-aware linter rules. That's a bit hand-wavy atm, since we're still working out the details of how the two tools would work together.
So we do want to provide more opinionated feedback about your code — for instance, highlighting when implicit `Any`s show up in an otherwise fully type-annotated function. But we view that as being a linter rule, which will likely be handled by ruff.