What does genetically tractable strain mean?
You've already basically got the idea of &quot;genetically tractable&quot;: if we can readily modify an organism's genome using known techniques, then it's genetically tractable.
That's a moving target, of course, because the set of available techniques is constantly expanding, so this is more of a pragmatic definition than a taxonomic definition. It's a notion that's quite important, however, because it's far harder to study an organism or to develop applications if you can't manipulate its genome.  If you can manipulate genetics, then you can make knock-out strains, introduce new functionality, and apply many, many other powerful and useful biological techniques.
So now to the last part of the question: assuming you've now got a tractable strain, why compare it with the reference strain? Well, if you're working on engineered applications, you probably really don't need to (other than from curiosity).  If you want to use the tractable strain to study things about the original, reference form of the organism, however, then you need to know their differences in detail, in order to have some idea of how much your results obtained by manipulation of the tractable strain are likely to inform your understanding of the reference form.