"NO CHANGE TO EGRESS, OCCUPANCY OR USE" is a remark related to the permit showing that the renovation work you are doing is not intended to change the egress, occupancy or use. If it was you there would be different requirements with the DOB, including a more detailed inspection related to the proposed change in either egress, occupancy or use.
If you call another lender and ask them if they would require the open permit be signed off on before closing a conventional loan. You will find that most (if not all) will have this requirement. If you think the lender making up the requirement ask them if they can show you what the underwriting requirements are with respect to permit.
Have you asked the lender if you can pay a fee to extend the closing date and keep the same interest rate. This normally done on purchase loans and new construction loans but might be available for refinancing.
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You are not the first borrower who has faced this issue.