The workshop is restricted to Weaponized Vehicles, which aside from the basic options (armor, respray, performance upgrades), feature custom options mainly available via Research, which can include liveries, armor plating and weapons.
Grand Theft Auto Online
In the Bunker, Facility and Nightclub, the player can modify the desired large vehicle (see lists below) by entering the vehicle in its parked location and select the customization option in the menu (default pressing right on the D-Pad) instead of accelerating to leave the storage area.
If the workshop has been added to the MOC, Avenger or Terrorbyte, selected smaller weaponized vehicles (see lists below) can enter the Vehicle Workshop module by driving them to the access ramp. Once inside, again the player can start customization by entering the stored vehicle or interacting with the mechanic.