I notice that when I go into MVAM mode Alpha, the hull sections are firing beam weapons, at least that's what it looks like. I don't have a single beam weapon on this thing...will I benefit from the Beam: target subsystems and Overload skill when in Alpha mode?
Not in quite the way you are thinking, Jdb2008. As the Beta and Gamma sections use beams while you're in Alpha, there will be *some* benefit for it, but their abilities are hard coded and can't be changed.
Realistically, if you're specializing for the two other sections you're not getting much benefit. In my opinion at least. If you right click on the MVAM console and scroll down to the section descriptions you should see a list of skills that improve the NPC sections.