Storage boxes: + modular, could be secured and weatherproof; - need to be a tetris master, may complicate load plan as items need to be accessed, can be expensive
Tonneau: + can fit odd shapes, keep items out of sight; - not waterproof (may help, but not solve water intrusion challenges), cannot bear load on cover
Lid: + can fit odd shapes, based on design may bear additional surface load; can be secured and weather-resistant; - can be the most elaborate/complicated design
Expanded steel top: + relatively inexpensive material; can secure contents well, can bear surface load; - no weather protection, design requires framing and reinforcement to bear a load
Does a lid need to be on/off or could it be segmented?
Perhaps a section before the boxes, a section the length of the boxes, then a section after the boxes to the tailgate.
Another option could be a rigid deck between the boxes and then hinged lids fore and aft... depends on what you put in the trailer.
With creative design, the lids could be removable entirely so you are not cargo-height limited.