It's a long story, so I'll try and give the simplified version.
The Ores mod, at one point, unsure if it still does, actually served more than just Bob's mods. It has been a method to get ores for DyTech and 5Dim, however, just because you have the mod installed, doesn't mean you automatically want all the ores.
The options in the screen choose if THIS MOD turns them on or off, but you can also turn them on in code. bobplates (Bob's Metals, Chemicals and Intermediates mod, or MCI for short) has another option in it (can't remember the exact name) and this is on by default. This option will automatically enable (Without changing the settings of the ores mod) all the ores it "Needs" to function correctly. Some of the optional ores like Cobalt and Sulfur aren't turned on, and others such as the water ores are turned on only in certain situations. (In the case of water, only if you don't have water recipes enabled.)
So in theory, the only ores you'll ever really want to turn on are Cobalt, Sulfur, and Water... though I tend to manually turn them all on anyway to make sure I haven't missed any, but in it's default configuration, it should still generate all the ores for any other mods that turn them on.
And no, you don't need cobalt ore, even though cobalt is used in MCI, because you can obtain cobalt oxide from copper ore in an advanced copper recipe unlocked via cobalt research. (and the only thing you can use cobalt ore for is making cobalt oxide)
