This strikes me as the wrong approach. Front End Dev can be but it not usually that great of a prototyping tool.
Doing it this way they'll end up spending time working on things that aren't designing (fixing css bugs, etc).
Also Prototyping tools overlap more with how many designers think (the tools are made for designers), while html/css/js overlaps more with how programmers think (the technologies are made for programmers).
I think you're right if the designers would only end up using code for their prototypes. One of the things I really try to teach is to use the right level of prototyping for what you're trying to test (whether that be paper, clickthrough, or code prototypes). The reality though is that you don't really need courses for paper and tool-based prototyping. Invision and other tools out there have done a great job in being quickly learnable and easy to use. Front end dev however is a different beast. But if you're designing micro-interactions and anything with a lot of motion it can be really tricky to do those without code. By teaching the designers to code, it allows them to cover all ends of the spectrum when creating prototypes. Also it lets them communicate with the engineers in a much deeper way - very valuable since Atlassian has been a very engineering based company for a long time.
Doing it this way they'll end up spending time working on things that aren't designing (fixing css bugs, etc).
Also Prototyping tools overlap more with how many designers think (the tools are made for designers), while html/css/js overlaps more with how programmers think (the technologies are made for programmers).