Its not that any law trumps the Constitution, or that the CG operates in any way outside of it. It is merely that the Coast Guard has not just federal law enforcement power, but Customs power as well.
Customs officers do not need a warrant to search or inspect someone on the border. Nor should they. Coast Guard boarding parties, however, are specifically trained NOT to abuse this power and for the overwhelming number of cases this is true.
For somebody to get a visit from a boarding party at night in a harbor is a very unusual circumstance already. They've got plenty to keep them busy and they don't go around rousting sleepy boaters just for fun. Something else was going on for them to do that.
I once knew a retired member of the Coast Guard who bragged to me how he liked to trash people's boats who mentioned the Constitution.
Whew, Thank you! :)
Something else was going on. See No. 154.