I think the only exception is Canadian registered vessel and Canadian citizens. We have checked in once in person when the vessel did not have a customs decal, had to pay the per check-in fee (customs user fee) rather than the decal fee as we were not the vessel owner.
The next year we requested the owner apply for the decal ahead of our arrival (I think the entire fleet now has decals) and were able to call in on arrival at Culebra. All Canadians onboard a US flagged vessel.
Customs office was easy to find from the arrivals/departure area at the airport in Culebra.
Our Canadian owned vessel will have a US Customs User Decal this summer on the Great Lakes. US Customs officers really insist on it for vessels checking in along Lake Ontario, otherwise they tend to give a fairly firm lecture that you will have one prior to your next arrival or you may be turned around. Never had that lecture from the staff at the SVI office but on the Great Lakes, they expect Canadian vessels to have one prior to entry. Makes check-in fairly easy for all involved anyway