My understanding is there is no requirement necessitating batteries be contained in a box(es). The reg speaks only to movement of as battery. 
Builder standards do not apply to preexisting boats which makes the use of boxes discretionary.
 
United States FEDERAL LAW             183.420 - Batteries
             (a) Each installed battery must not move                             more than one inch in any direction when a  pulling force                            of 90 pounds or twice the  battery weight, whichever                            is less, is applied  through the center of gravity of                            the battery  as follows:
(1) Vertically for a duration of one                              minute.
             (2) Horizontally and parallel to the                               boat’s center line for a duration of one minute                               fore and one minute aft.
             (3) Horizontally and perpendicular to                               the boat’s center line for a duration of one                               minute to starboard and one minute to port.
The commercially available plastic battery boxes                       may be used to install a battery; however, it may be necessary                       to provide means within the battery box to prevent excess                       movement of the battery. The materials used for  restraining                      battery movement within a battery box  should be selected with                      regard to potential  deterioration by the electrolyte. The                      battery box  must be fastened in such a manner that the battery                       installation will comply with this section of the regulation.
Obviously, boxes properly secured offer better protection than with no box(es) but often logistics and space limitations make them problematic.