Re: Darwin to philippines (indonesia)
The complications are the reason we went with the rally from Darwin (we are not rally folks generally). They arrange all the paperwork. The CAIT is the prettiest piece of bureaucratic paperwork I have seen with fancy stamps from immigration, customs, the navy, Miss Indonesia (OK, I made that one up).
When we arrived in Kupang a boat came out from the shore and three of the nicest officials you will ever want to meet checked us in, with fairly normal amount of paperwork (You get the CAIT and other paperwork in Darwin). One of the officials even wanted a photo of us and her on the boat that another official took with her phone. They then asked us to go to a particular building ashore in the next day.
We thought we were checked into the country already, but no. In the building there were 20! officials busily stamping things and filling out forms. You went from desk to desk (immigration to health to port captain) handing out copies of boat regn, crew lists, passport photocopies (you do have many with you of course). Also, you positively need a boat stamp, if you don't have one they ask you to get one on the main street of town (about a dollar for the stamp and a dollar for the ink pad). Then you stamp all the forms beside every place you sign or initial. One American guy had one of those embosser stamps that lawyers use (he was a dentist so go figure). He was really popular as all the officials came over to see and feel the stamp. I assume if you are cruising independently you would have to find all of the various offices to do this stuff. I could imagine a good day plus to work it out (English is not commonly spoken). When we left Indonesia in Bali it took me the best part of a day to do the check out. This included an official in one office putting me on the back of his motorcycle to take me to another office that was a few km away and then waiting around to drive me to the next office on my list.
Everyone in the country was as friendly and accommodating as possible, but the bureaucracy boggle the mind. I get a sense that in many developing countries they are graduating a lot of people from college programs and that there are not enough jobs for all these folks so they end up working as bureaucrats in government. We saw it everywhere from Panama to Indonesia to South Africa. In Vanuatu we filled in a form that was 7 or 8 pages long. When we left we filled out the same form - the only difference was a checkbox at the top of the page for Incoming and Outgoing. They had so many forms that all their filing cabinets were full and they had piles of overflowing boxes on the floor. Just the way it is.
Finished the circumnavigation in early February in Grenada. Have to work on a book project for the next several months so the boat will be waiting for next year.