For Commercial loans (with commercial purpose) secured by a primary residence, do the late fees fall under any state statutory limits? Or would Reg Z potentially apply for that matter?

For state specific - there are no statutory limits on commercial loans that I know of.

Here is the info on consumer loans:Late payment charges are governed by Section 138.05(3), Wis. Stats. (PDF: external link), on purchases for individual, family or household purposes. Finance charges on consumer transactions are regulated by the Wisconsin Consumer Act.

As far as regulation Z if it is a commercial loan it is exempt from that rule:
Sec. 226.3 Exempt transactions.

The Federal Reserve Board's Regulation Z (12 CFR Part 226) has been republished effective December 30, 2011, at 12 CFR Part 1026 as one of the regulations transferred to the Consumer Financial Protection Bureau under the Dodd-Frank Act. This section of the FRB regulation was republished as §1026.3 of the Bureau's regulation.

This regulation does not apply to the following:

4 [Reserved]

(a) Business, commercial, agricultural, or organizational credit.

(1) An extension of credit primarily for a business, commercial or agricultural purpose.

(2) An extension of credit to other than a natural person, including credit to government agencies or instrumentalities.

Hope that helps!