ive not had the chance to repeat the process or test other setups yet (will set up a VM and do dumb stuff with it once i get my main machine back up 100%) BUT, my guess is it likely has something to do with how the ix-applications folder is set up and where its located. For me, i let the applications essentially self generate that folder on my main storage pool without creating a specific data set for it. And i think in creating it with that setup, much like docker would, it preserves all the configurations and settings in the Storage pool (as that part isnt touched in an install until you import it, and even then, it isnt modified in any way).
My guess (without a lot more trial and error) is that those who have experienced a different result, had their ix-applications folder that was wiped when they reinstalled, or existed on another storage pool or drive than what was carried over). Again, this is all speculation as Ive only experienced this situation once and have since lost the ability to talk directly to the guys at truecharts to pick their brains on the hows and whys.