When I swap to Toon3, what if I am hitting LEFT CTRL+Y for something random? How does that affect the LEFT CTRL ? Or does it?
Doesn't matter.

These modifiers are used for exactly 3 keys: FTL Target Me, FTL Assist Me, and FTL Follow Me. Anything else you do is unaffected by the FTL modifiers. When you use (or one of the other mapped keys uses) one of those 3 things, the selected FTL modifiers for your current character are sent with the key selected for that particular action. So for example if FTL Follow Me is set to F11, and the FTL modifier is Ctrl, then it's going to press Ctrl+F11 instead of just F11. This essentially uses a different macro in the game depending on the character, so each guy knows who to assist, target, or follow.

So no, it doesn't matter if you are pressing Ctrl+Y, that is unaffected.