Did they? Aren't the preorder bonuses just some normal unlocks unlocked at the beginning?
The preorder "Limited Edition" bonuses are just early unlocks for weapons in the game.
They're going to have an online-store component where you can purchase stuff, what exactly we don't know yet (extra maps? new weapons? new skins for weapons?). It's going to be like ME2 where some stuff is free and some you'll have to pay for. Console gamers who purchase the game used will need to pay for stuff that people who purchased a new copy got for free.
As for the mod tools, I don't ever expect to see them for this game, and without public server code it won't amount to a hill of beans if someone figures out a way to mod the game without said tools.