I've flown from Bali to LBJ/Flores using WINGS/LION air
In terms of checking in the over-limit luggage, as you have probably found out, it is quite easy to sort out once you are there. They will weigh your bags (make sure they write the correct weight on the papers) then you will need to go pay for it at another counter. Once paid, you need to complete the check-in (sometimes you have to line up all over again, or sometimes you are able to jump the line) - perhaps allow time for this.
The flight, on the other hand, was a bit of a circus...
As the boarding time got close, it was officially 'delayed' for an hour. The new boarding time came... then passed with no details.. then there was a sudden change of departure gate with a "final boarding call" where everyone madly rushed.
Once on the plane, we sat there for 45minutes (no air-conditioning), then was told to disembark and return to the departure terminal, where we were not told of any details regarding the next departure time (if at all), except that the flight was 'cancelled'. (We were quite worried as we had organised a taxi/boat to pick us up at an assigned time) and were only going to be at Komodo for a few days.
Besides getting some help from a friendly local who let us use her phone to make some calls, and an attempt to book another flight using Garuda (quite expensive, and the internet was poor), the wings staff brought some local foods and drinks for those who were hungry (which was kind of nice..)
We eventually boarded the same plane and took off, where we arrived a few hours after our intended arrival. The taxi/boat were patiently waiting for us, and we missed a check-out dive...
Upon reflection, and from other research, Wings/Lion Air seem to regularly miss their take-off windows, so essentially we just had to wait for the next opportunity. I assume it meant bumping the next flight to the later window, and so on... (This is probably why they have been 'black-listed')
So as per advice from
@mattia_v I'd recommend booking the earlier flights, so that if things didn't goto plan, you will be
put on following flight. Perhaps even avoid arriving on the same day as the boat departure.
In comparison, the return trip was fine. This is probably due to there being less flights out of LBJ, and the next take-off window comes sooner if they are running late.