<p>I would lean towards allowing such questions.  For example, I answered such a question here: <a href="https://stats.stackexchange.com/q/162996/7290">Difference in output between SAS's proc genmod and R's glm</a>.  My general position is that whether a question should be viewed as off topic should be determined by what the OP needs explained: if the required explanation is statistical, it's best here, but if the required explanation is the code or about how the software works, it should be considered off-topic here.  This rule usually leads to an unambiguous decision (although it may be opaque if you aren't familiar with the software or the statistical concepts at issue).  There can be a gray area, though.  When statistical software is designed, default choices are made by the developers that are statistically important.  Often users will use the defaults without much thought or even being aware of them.  In some sense, the answer could be, 'read the documentation for the two systems and notice that they make some different default choices'.  But in another sense, to answer such questions well really does require <a href="https://stats.stackexchange.com/help/on-topic">statistical expertise to understand or answer</a>, and constitutes a <a href="https://en.wikipedia.org/wiki/Teachable_moment" rel="nofollow noreferrer">teachable moment</a>.  So this is an area where I will typically leave such questions open if they aren't egregious.  </p>
