I can see silent pings from enemies.
Starbases don't upgrade with Alloy on.
With Alloy on, you get serious +/- cash and resource fluxuations and can buy when you are in the red.
You can also start research and build structures in the red with Alloy on.
I have noticed that if you have a cap ship and some frigates that you give an order to jump, the frigates sometimes don't get the command. At first I thought it was me, but after it happened a few times, I have come to the conclusion they aren't getting the orders properly.
Balance: TEC got SHAFTED with the mines.