Why shouldn't I bake on scratched silicone mats?
Silpats and Exopats have a glass fibers (regionally called fiberglass or glass wool, but not candy floss) embedded in them for strength.

The warning not to use them when scratched is because fiber glass does nothing good for a person when ingested, and a scratch may expose it.

Some types of silicone based cookware do not have the fiberglass reinforcement, and so do not have the same issue.  These are mostly the flexible baking dishes or muffin cups, but you should read the label information for the product you have.