Are there ways to get extra credit for products that exceed the thresholds?

Yes, several ways. For Options 2 & 3, The local materials multiplier doubles the value of products that come from within a 100-mile radius of the project, but the raw materials have to be local as well, not just the manufacturing. For Option 2, Cradle-to-Cradle Gold or Platinum certification gets you 1.5 times the value. And for Option 3, products with documentation going farther up the supply chain (beyond the immediate, first-tier suppliers to the manufacturer) and with documentation for ingredients below the standard threshold get extra credit.

Does Cradle-to-Cradle’s Material Health certificate count, or only full Cradle-to-Cradle certification?

For Option 1, either one counts if the product is certified at the Bronze level or higher, although for the Material Health certificate to count it also has to indicate that at least 90 of materials have been assessed. For Option 2, just full Cradle-to-Cradle certification (Silver level or higher).

Yes, the credit language includes information about other certification levels for Cradle-to-Cradle v2, but those certifications have all expired by now, so you can ignore those details.