I don't know if I'd just write it off like that . Musicals tend to deal a lot with characters' emotions and personal issues, so I wouldn't be surprised if we got some fairly significant developments in The Flash episode. Just look how important Once More, With Feeling was to Buffy's story arc.
Once More with Feeling is a huge exception, in my opinion its the only good non-animated musical. But, I think Flash's will be more like the second of the two unwatchable musicals Xena had (specifically Lyre, Lyre Hearts on Fire). That was just a bunch of badly done licensed songs in an episode that had no point and with a stupid story on top of that. That seems like the kind of musical Flash will have, except it might mention some elements of ongoing plots. Besides, I imagine they know they'll have a chunk of their audience tuning out for the musical, so nothing big will happen. Even Buffy didn't put any story changing things in the episode, just a few revelations about character relationships, and Flash doesn't have any stuff like that at the moment.