This is something that has bugged me for some time now, too.
Yes, using the bypass launches 2 of them, but as it stands you're physically launching "4" flares worth of slots, instead of only "2".
In the FA-18C.lua line 206, the flares are set to "chargeSz = 2" where as chaff are set to 1. Modifying it to 1 will allow you to hold up to 120 flares just like chaff, which you can then manually release all 120 of them 1 by 1 using a single release profile on the ALE-47.
Either the in-game model is incorrect and our latest model of the F/A-18C is for whatever reason stuck using a MJU-7, like the lua says. or they're incorrectly modeling our flares. /shrug