There are a couple of key missing items here to come up with the right  answer. One is clarification of the facts. Presuming the loan was for the purchase of the land and a manufactured home, which was moved onto the property shortly after the closing, the lender should have made that part of the closing instructions and there should have been  later  disbursement of funds (to add the building to the property ) the disbursement would  have been obligatory... meaning there would be a claim for the lender as the house was clearly intended to be covered in the loan as real estate.

Most importantly, WHICH policy was issued. The Standard ALTA Policy is intended for land without structures, but with the Form 7, I would still file a claim. The 2008 Expanded Lender and Extended Owner's Policies have specifically added language  that would clearly make them liable for coverage, even if they listed the covenant as an exception. 

The 2008 Homeowners Policy under 12 & 16 provide coverage if you are forced to correct or remove an existing violation of any covenant.... The 2008 Loan Policy  No. 11 a and 11 c , talks about disbursing of funds for improvements.

I think you very likely have a legitimate claim. Let us know how it turns out.