(Takes a deep breath...)
OK, let's take this step by step, and compare your set-up to mine. In the MFD, I've set up my lock/unlock options so that a single press on the unlock button on the remote unlocks ALL doors and the boot. However, if I don't open a door or the boot within something like 30", then the car locks itself. A sensible precaution so that an accidental press on the remote doesn't leave the car unlocked.
Now, having unlocked the car, if I open a door or the boot, the car remains unlocked until I decide to lock everything with a single remote press. I can open and close the boot/doors any number of times, and everything remains unlocked - which (for me) is how it should be...
Now, you've said this: "I'm particularly concerned by its relocking itself when the doors are locked though, because of the potential for leaving the keys inside. I find it difficult to believe there isn't a way of over-riding that, but I haven't found it yet."
It seems to me that you need to find a setting where everything remains unlocked until, and only until, you choose to hit the lock button the remote. In that way, you can never lock your keys anywhere within your car as you would need the remote to do this, which is attached to the keys. Am I getting warm?