There are times when the "convenient" joints do not line up... I've had that happen, since my layout is all sectional track, but some custom curves done which has changed the "lineup" of joiners. Since I use SJ rail clamps, it's no big deal.
I would not be so quick to jump in here, but it's clear we have confused Sarah before with conflicting answers... so trying to help her the best...
Regards, Greg
p.s. if/when she does employ a reverse loop module, the "detect short type" won't care, but the ones that want an independent sensing section will mind I believe, so striving to line them up for the future is indeed not a bad idea, I agree.