Whenever any person shall have proceeded without the permission of the Board to do anything which, according to the terms of this chapter, requires such permission in any form, the Board may, nevertheless, grant or deny such permission, in whole or in part, as if such thing had not already been done or commenced; and, in the case of a denial by the Board of any such permission, the Board shall make such order as it may deem appropriate requiring the modification or removal of any structure or the undoing of any thing constructed or done without such permission, and such order shall be enforced by the Superintendent of Buildings, and any violation of any such order and any failure to comply therewith within any reasonable time for compliance therein set forth shall constitute a violation of this chapter. If the Board finds as a fact that the thing done without the requisite permission was done in good faith and in an honest belief that the person doing the same was entitled to do the same, the Board shall set forth such finding in its decision; in any such case where the permission is nevertheless denied and an order issued requiring the modification or removal of any structure or the undoing of any thing, the Board shall require only the minimum modification, removal or undoing which the Board deems necessary to effectuate the purposes of this chapter and shall state in its decision that the requirements in its order contained are such minimum. Where the Board does not find such fact, it may require such modification, removal or undoing as it deems appropriate under all the circumstances to effectuate the purposes of this chapter and the policies of the Board not inconsistent therewith.