Probably legacy reasons. Flash SMS was designed in a world where phones had teeny-tiny amounts of storage. So there were regular SMSes—that were only supposed to be ACKed once they were persisted to disk (or to the SIM card!); and then there were flash messages, for realtime, ephemeral, if-you-miss-it-it-doesn't-matter messages. Sort of the textual equivalent of RTP packets.

It probably made more sense in the days when carriers closely controlled the phone's UI and there weren't other apps that could be interrupted by such a popup.