So, I understand the risks that antimatter storage could incur... but consider the following scenario: you've been fighting a highly successful campaign, striking down and disassembling a multitude of UFOs. Your main base is packed to the gills with the stuff, when it simply blows up. As antimatter cannot be produced by the player, it's rarity may end up much like that of Elerium, meaning that any loss of it, including a voluntary one, cannot be properly replaced and could be catastrophic. A random chance of blowing up the base would put a damper on what could potentially be a highly influential resource: either you throw some away, or it all blows up. Most likely, players would just keep it all, and load game when their base explodes.
On the other hand, I love the idea of the destruction of an Antimatter storage facility destroying the base. I'm leafing through the code now, and I don't think this will be particularly difficult or unbalancing. Realism may be a positive thing, for once...
In fact, I'm going to go ahead and code that in as an in-house modification, and play a couple dozen games with it. I'll try to let you know how it turns out.