Please place the following under GameUserSettings.ini in your Atlas game folder
If you don’t do this the ships will not allow structures.
Also read the settings instructions carefully...

To configure your singleplayer experience you must enter the following under
(Where the game is stored) \Program Files (x86)\Steam\steamapps\common\ATLAS\ShooterGame\Saved\Config\WindowsNoEditor

Open the usergamesettings.ini via notepad++ and add the following commands at the bottom...
(feel free to change the settings to your liking)

[Ship+] (this must be placed with the info under*)
Current INI V26.1
[Ship+]
Smithy+CraftingSpeed=2.500000
Smithy+CraftingSkillQuality=-1.000000
Smithy+CraftingRequirementMulti=1.000000
Smithy+ItemStackMax=50000
Smithy+InventoryItems=600
SchoBaseWeight=9000.000000
SchoBaseHealth=10000.000000
SchoSailUnitMax=5.000000
SchoStructureHealthMultiplier=0.500000
SchoNumberofBeds=2
SchoNumberofCrew=20
SchoMaxSaddleStructuresNum=280
SchoMaxSaddleStructuresHeight=1100
RespecGoldAmount=2500
SchoCanRespec=True
SchoMaxShipLevel=60
BrigBaseWeight=15000.000000
BrigBaseHealth=20000.000000
BrigSailUnitMax=8.600000
BrigStructureHealthMultiplier=0.500000
BrigNumberofBeds=4
BrigNumberofCrew=20
BrigMaxSaddleStructuresNum=420
BrigMaxSaddleStructuresHeight=1100
BrigCanRespec=True
BrigMaxShipLevel=60
GallyBaseWeight=30000.000000
GallyBaseHealth=40000.000000
GallySailUnitMax=16.000000
GallyStructureHealthMultiplier=1.000000
GallyNumberofBeds=2
GallyNumberofCrew=59
GallyMaxSaddleStructuresNum=615
GallyMaxSaddleStructuresHeight=1100
GallyCanRespec=True
GallyMaxShipLevel=60