No, not as currently designed. The plugin support was designed to allow plugins to add results, not to allow them to replace results. For example, a plugin can produce new diagnostics that are specific to users of a package, but they can't remove diagnostics produced by the server. They could provide navigation for regions that server does not provide navigation for, but cannot change what server would produce.
I really like that idea. It seems to me, though, that it would be better to provide support for this in server directly so that all code generators could take advantage of it without requiring every author of a code generator to also author a plugin.
One possible way to do that would be to define an annotation that code generators could emit that would tell the server that navigation to that element should be redirected to a different location. Perhaps something like
@RedirectNavigation('relative/path/to/target', offsetInTarget)
void someGeneratedMethod() { ... }
Would that work for your use case? What do you think?