OK as I understand it from rooting around in the gameinfo folder, the way gameplay speeds are currently implemented is that all aspects of gameplay are speeded up. Look at the end of the gameplay constants to see what I mean. However I don't see an antimatter regen scalar in there, and if not then that means that colony ships will be colonising at the old slow speed, while your ships are clearing planets faster. This also *seems* to actually be happening. It seems like I'm clearing way more planets than I'm colonising, more than I used to.
Also, I'm not seeing a weapon/ability cooldown in there either, so ships will be moving faster, but not firing any faster. This could lead to an ability to retreat easier, etc.