I figured it out. What was causing my problem was that the mapScripts: needs a second addCraft command in case the shape of the ship is not a 1x1 map block.
mapScripts:
- type: STR_MFTD_ARMSWAREHOUSE
commands:
- type: addCraft
rects:
- [1,1,1,1]
label: 1
- type: addCraft
rects:
- [1,1,1,2]
conditionals: [-1]
- type: addBlock
size: [3,4]
There is no need to define the vertical placement of the craft it automatically places it on the first floor terrain from the top of the map.