Close reason "This question does not appear to be about a specific programming problem" listed twice

The short answer is that you are correct that "they used to be two different close reasons but were edited"

If we look at an archived version of the page you can see that it was closed under a split 2-3 vote. Two votes for Server Fault and 3 for Super User:

A big part of the rationale behind retiring the Super User and Server Fault closure reasons was because there were (and are) many off-topic questions that fall somewhere in between or totally outside the scope of either of those two sites. So we created a more general off-topic reason which allowed users to close off-topic Stack Overflow questions without needing to pick somewhere else where it would/could be on-topic. This is especially helpful in an age where the network is much larger than just the trio of sites.

As part of the process for adding the new reason, it was decided that the old closure reasons for Super User and Server Fault would be edited so that the banners matched the new "Not about programming" reason. V2Blast, a former Community Manager, handled updating the old text, deactivating the old reasons, and enabling the new closure reason.

Rolling the changes out like this was basically a way to automatically "update" all of the old Super User/Server Fault closure banners to reflect the newer, more general closure text without having to reopen/reclose a large number of questions.

At scale, this was determined to be the most effective way to make this change. However, we do end up with a small number of edge cases like the one shown here. Unfortunately, the only (viable) way to fix this would be to reopen and reclose each individual question that was impacted by this change.