Well, being a Guam sailor, I can tell you that we had everyone belowdecks (bridge being the exception) way before we hit the breakwater, and that transit from peirside to breakwater doesn't take long at all. I don't understand why they wouldn't have just putted along and pulled everyone in prior to leaving the harbor...unless the CO was in a major hurry. That is the only way I can see them leaving people topside, even though there is no reason to do that.
Maneuvering watches out of Guam were a whole lot shorter than anywhere else. As soon as topside was stowed, we'd wave that the ever-present Russian fishing trawler, pull the plug, and disappear into the Marians Trench.
Being in an unfamiliar port, they probably kept the pilot on a little longer than a boat that was home ported there. Also looking at that harbor via Google Earth, it looks as if you have a few tricky turns just before you enter the sound and approach the breakwater. My guess is that they were disembarking the pilot, (which is almost always done from topside on 688's, not the fairwater planes) and then rolling the forward cleats. Even that little bit of work takes 5-10 minutes, plenty of time to get into trouble.