DONK,

Which Code and/or Regulations apply?
If the Ship construction is supposed to be in accordance with the American Bureau of Shipping regs (ABS), then you should inspect for warpage tolerances as allowed by the "Shipbuilding and Repair Quality Standard for Hull Structures During Construction" For example, the max warpage limit for a Bulkhead inbetween stiffeners is 8mm.
Flat plate warpage in ship construction is unavoidable and caused by many things other than just welding side-effects such as Girder shrinkage, improper fit-up, and compression loading.
Fortunately, excess warpage is easy to fix by a number of methods such as slotting and heat shrinking.
Unfortunately it is a constant battle to keep warpage under control and having to force a reluctant fabrication contractor to perform rework is a hassle.
Of course there are steps that can be taken to minimize warpage, such as the sequence welding you mentioned. This is especially helpful while using the FCAW process. However it is very difficult to get most Shipyard Welders to move around that much while no one is looking over his/her shoulder making it happen.
My opinion is that the benefits of using the FCAW process for this application far out weigh the detriments.
Good Luck!
Tim Gary