In Commercial-Industrial Development, the total project cost includes all costs incurred during construction and through the lease-up period. The permanent loan term begins at the start of the lease-up period, so its terms affect the total project cost. If the amount of the development loan is set based on the total project cost, it will thus be affected by the terms of the permanent loan.
You may choose to have no lease up period or you can set its length to any number of months in row 211 on the Development worksheet in the Classic Mode or manually configure the lease up of your tenants in Monthly Mode.