The only problem is if you inadvertently run a crafting macro before starting the craft by mistake. You could end up with a situation where it was still running invisibly in the background & you try to start a craft when it's at, say Byregot's, resulting in a ruined craft. You wouldn't have a way of telling as some actions may have still to occur but be delayed by a <wait.x> command.

I do sympathise though, it's a real pain. Even being able to adjust the sound, location & size for that particular alert separately would help. You could make it small, silent & in a corner without running into the problem I outlined above.