Hi,

It would be nice if default setting was the same in different suites.
 
it's a nice idea of course, but I feel it is impractical as it would require changing a lot of software, both modern and legacy. 
However, given array of flags it is algorithmically trivial to figure out what is test and work flags. That's what phenix.refine have been doing since its beginning (2005). And my understanding is that Refmac does this too. As always, there are corner cases here, but it's better than nothing. Plus, programs (at least phenix.refine, can't speak for others) tell which flag was actually used, and they provide option to define the flag value to use.  

Pavel