There is a limit of 2000 notifications. We should first double-check we actually still need such a limit (it says, "What we gain from this is we could run expensive queries otherwise that would requires adding index and data denormalization.." but that comment could be stale).
If we do, @Mooeypoo suggested splitting the count. E.g. 1000 each of alerts and messages (or 500 alerts, 1500 messages), so a flood of alerts can't clobber your (more important) messages.