Hi Russ,
I'm with you on the overlapping bases vote, but I was unable to convince my colleges to vote with me (as they were going for as little changes as possible). But it's not a mess!
Torps can hit a ship hiding in a large base, but they'll hit the big base first.
Defences can stack!
Massed turrets when combined in such away as Necron escort squadrons stacked on capital ships can get into the crazy numbers of 10 or more turrets easily with little ill effect. So the +3 limit was imposed.
On the point of rewriting the rulebook- an unofficial copy incorporating the FAQ would be a great work of human civilization!

When this FAQ is 'fixed', I can really see this happening, if I can get a few volunteers!

Cheers,
RayB HA