As redricky said, if you want to optimize your torps - it's going to be a case of avoiding autofire. This was the case even before the Omega Torp. Even with 3 Green PWO-T's, if you had 4 torps - that 4th one would be unlikely to fire. If you tried to squeeze in a Tric, Cluster, Harp - it might never fire - regardless of where you slotted it. With better PWO-T's, you could find that even the 3rd wasn't firing on occasion - it just isn't efficient with autofire.
It would be nifty if the Left->Right thing offered precedence, so that it checked - but I'm not sure that's anything they're going to look at any time soon - since it can be resolved with a keybind and is not something completely broken.
It's kind of like how mapping fire torps to spacebar doesn't work as well as mapping fire phasers does - that's very annoying too, but again - there's a fix for it so it's not likely high up on their list of things to look at...
That isn't true at all. I've flown my B'rel torpedo boat for several months. All of my fore and aft torpedoes fire, with autofire, and am usually cloaked again in less than 6 seconds.
That may not be the case with the Omega and Romulan plasma torps, considering who it screws with the timing. But, with my current setup, everything fires as it is supposed to.