There is probably a lot to discuss about Test and NativeCall module versionning. Since there are not really part of the language themselves they can be decoupled from the language version, but at the same time they are an important part of the functionnality a perl6 bundle provide you so tt's probably not an easy anwser.
Anyway 6.d is probably the occasion to fix this but also fix or address some issue that exist with the current NativeCall.
My experience with NativeCall is tied to the writing of a binding module (Gumbo), some work on DBIish to introduce more perl6ish method and the writing of GPTrixie, a NativeCall code generator.
I also had some work in the NativeCall.pm module itself (type checking for sub signature and ABI version for lib) and some lowlevel stuff (bool and size_t type)