Monkeypatching, dll injection, Jar Classpath - Huge sources of pain. It Is how it's done but in certain contexts any benefit is immediately outweighed as the bugs start accumulating.
Right, in certain contexts (I would even say most contexts) it can be a problem. However, it's not obvious to me that this—a well-defined interface for injecting plugins that's specified by a library that functions as low-level infrastructure—is one of those contexts.
It needs to be scoped to the dep so conflicting deps have independent dependencies.
If foo 1.1 takes a dep on Bar 1.2, and baz 2.3 takes a dep on Bar 1.4, both Bar contexts are tested with their respective libraries but forcing Bar to a particular global version can have problems and both versions of Bar are needed to have tested behavior.
Examples mentioned and OP change the global behavior vs proper dependency management.