This doesn't sound unreasonable to me. Leaf dependencies may need to know which runtime/back-end/OS API to use, but these things aren't just implementation details. They may affect things like operating system compatibility or cause performance issues that affect the whole binary.
Only thing I'm worried about is fragility of such configuration, similarly to how patch.crates-io section is fragile and can cease to apply at any time. For example, I may want to make HTTPS requests with a specific implementation of a CA certificate store. I'll configure fooTLS library to use it. But if my requests library changes its dependency to barTLS library at any time, my fooTLS config won't be applicable any more.