Both professional and amateur astronomers/astrophysicists use a lot of software either for image processing or data analysis. So should queries related to those software be allowed here as well, even if software specific SE (Mathematica, Matlab, etc) exist?
If it's a general question about said piece of software, then probably not - but if it relates to astronomy in some way and there's a good chance the expertise needed to answer it would be on this SE site, I think such questions are perfectly valid.
I think they should be allowed here. There has been and will always be some overlap in contexts (ie. astrophysics and any specific/general software here). Topics shouldn't be restricted to have some other contexts as well, but the only restriction should be - It must have a relation astrophysics. - This makes this site complete, which is more important than having a question here with less to do with astronomy than to something other. This also lets users of this site gain knowledge or solve problem in case they are unaware of or do not want to go to stackoverflow for any reason. The goal should be to unite and provide a source of information for astrophysics and astronomy. Some looseness in the subject should not be given so much importance.