I don't know how other operators do it, but for Singapore 02L and 02C, which have a "ship crossing" problem, we carry several RTOW pages for each of these runways for a range of ship heights.
ATC are very good at advising conflict times and the height of the ship, thus enabling (even at a late stage) crews to revise Takeoff data. Most Takeoffs are at Derated and/or reduced thrust, thus the shipping conflict is quickly resolved by using higher thrust.
The problem is when the aircraft is already at maximum "non-ship" RTOW, and no performance enhancement is possible, then the only solution is to wait whilst the ship chug, chug, chugs out of the way.
Top marks for UAL, they just rose a few points higher on my "will fly with" list.
Regards,
Old Smokey