This is possible in OXCE if you make the other human faction's craft a separate terrain:
mapScripts:
- name: STR_SCRIPT_WITH_3RD_CRAFT
commands:
- type: addCraft # player craft
- type: addUfo # alien craft
- type: addBlock # other faction's craft
size: [1, 1, 4] # should be equal to [x, y, z] size of the craft
verticalLevels:
- type: ground # places the LZ
size: [1, 1, 0] # 0 height means next level will be right on top of this, x, y are the same as the craft
groups: 1 # LZ map blocks
- type: middle # places the craft
size: [1, 1, 4] # size of the craft
terrain: TERRAIN_FOR_THE_NEW_CRAFT
The caveat to this is that it doesn't work quite the same as the addCraft/Ufo commands; the mission terrain needs to have a group 1 mapblock the same width and length of the craft's map, it can't just fill 1x1 LZ mapblocks underneath for larger craft.
Edit: Ninja'd by Solarius, but I want to add a remark about that - the terrain tag used in tandem with addCraft/Ufo will only change the LZ underneath the craft. However, if you make the new craft map with its own floor so it doesn't need LZ blocks underneath, then you can just use the terrain tag with addBlock.