Is there any concern about a web-native journal being less "future-proof"? I've come across quite a few interactive learning demonstrations in Flash/Java that no longer work.
This is a high-priority for us. By focusing on web-standards and avoiding proprietary plugins we're pretty confident that the content will be future-proof.
Something that could help is perhaps a choice that examples should work in (e.g.) Firefox recent.x on ubuntu, then provide a VM and archived version of firefox. Put it on a platform that archives things with C/LOCKSS and get a doi, then although you're not expecting people to use it on a daily basis, it'd cover several "worst case" kind of scenarios.
Of course that's not completely permanent, but would perhaps provide some more safety.
I feel like binding the journal to GitHub means that it's less likely to exist over the long term (where long term means >100 years, which is as long as I would expect an academic article to be accessible for).
We produce "archive html" files where everything is bundled into a single file. We're looking into ensuring their long-term preservation with projects like LOCKSS.