I'm building https://starboard.gg, it has the same issue. The iframe is important for sandboxing user code, and alert is often used in tutorials (despite being bad practice, it's intuitive for beginners).

It'd hardly be even minor effort for the repl.it folks to just include a file in their sandbox loader that gives folks a normal, modern modal when some JS contains prompt() or confirm().

Remember: it's not about whether it's useful, it's about whether there isn't a better way to do it, because it's useful. In this case: yeah, absolute. There are way better ways.