MCT at KUD - 15 mins doable?
 

I think you should able to make it, since it is an extremely small airport, and most likely it is the same aircraft that connect to BKI

I'm not so sure. You may be treated as a no show as the handling agent for these "rural" airstrips is usually some local folks, maybe a travel agency guy etc, and you - not just your luggage - need to be weighed at check-in. Hence, physical presence is a Mandatory!. From my observations, most of the check-in formalities are done well before the Twin Otter lands - given that it is on the ground for only 15 mins or so. However, as the process is done manually, there *may* be some discretion to allow "late-comers" to check-in - but bear in mind that the folks who handle check-in formalities would be the same folks who would offload baggage from the flight that would have just arrived and would also be responsible for putting new luggage on the plane. There would be time pressures. So, I would understand if there would not be anyone to handle check-in after the incoming flight has arrived.

The on-the-ground-time in KUD may be a very, very short one or a slightly longer one which allows the pilots to go for bathroom breaks in the tiny terminal.

I think here's what you need to do without having to worry about being treated as a no-show.

The aircraft originates in BKI. It goes to KUD and then off to SDK before turning around back to KUD and then BKI.
You should be booking BKI-KUD and then KUD-BKI as two separate tickets. You would have about 2+ hrs in between.

Use that time to go into KUD town and have a brunch or a walkaround or both - it is a very small town. There would be local taxis waiting outside the terminal for the arriving flight from BKI. Make arrangements for them to pick you up from town about an hour or so later to take you back to KUD terminal for the return flight to BKI.

If you have time in your travel plans, spend a day or two in Kudat. It's an interesting area (not the town itself tho). I'd highly recommend a drive or a stay near the Tip of Borneo. I love that place so much and I would love to go back.

Would like to do this, but don't have the spare time at the moment. I noticed the re-scheduling had at one point put a BKI-KUD flight on a Sunday and the KUD-SDK on a Monday, so was going to try at least a 20 hour stay
but they've since re-scheduled again to remove this flight from the schedule entirely.

I'm not sure why they've removed the option to book a through-ticket; I get that it's a subsidised Rural Air Service but that fare worked out more than the direct BKI-SDK flight, and had a much more convenient timing too.