BF two of my Komodo trips have been Bali-Bali (love the convenience and adore Mermaid I).
I usually pleasantly identify the luggage as SCUBA gear right away and almost always the ticketing agent has given me a few kilos beyond the limit. My primary worry is always making sure the luggage makes the flight. I am happy to pay overage if I can stay on the good side of the ticketing agent. (Of course as is true everywhere, paying overage does not ensure one's luggage will make it on to that flight.) Last trip to LBJ I didn't try to negotiate much, partly because I was trying to help a stranger at the same time. I paid for the amt listed on the slip - under $20 US (equivalent) total, each way. (This was the trip 5 divers did not get all their luggage.)
Roughly the same two trips before that (< $20 US each way) from Bima.
One of my first flights out of DPS back in 08 the ticketing agent offered to settle things at the counter. Definitely what he had asked for was less than what I ultimately paid through the office (I was young, naive, and had no extra USD at that point).
Re, ferry, it is true, delays are frequent in domestic Indonesian flights. In my experience cancellations are less frequent (touch wood!). But my thinking is if I book the flight the majority of other guests will be on (frequently arriving the day of the cruise - I always check with the LOB for this) if there is a cxn, the boat should have to wait if a large enough group is stranded. I have also arrived e.g. in Sorong a day or two early and just relaxed, but in LBJ the hotels will generally be more modest than in Bali or Jakarta. For me, the ferry would be the least relaxing of those three options. I have taken ferries in the Philippines (not Indonesia) and they too were prone to delay, had issues with safety, and were very time consuming. YMMV of course but in all the trips I have done, I have never met anyone who ferried over to LBJ or Bima. I am not sure scheduling that would work. I did meet someone who considered buying an extra ticket for their luggage next time - but it was still less for them to pay the overage.
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