Anthropologist Beverly Strassman gets it. She basically said “yeah, it’s not scientific - BUT there’s a reason for the narrative, and it’s beyond science.” (I’ve paraphrased, but the reference is here).
Basically, periods aren’t fun. So a 2016 research paper speculates that the reason the myth still exists is because menstruators want a sense of community - and this community is hard to find because of how taboo it is to simply talk about periods. I’ve also found this myth cropping up the most often in workplaces - where menstruators have to ‘get through’ the day when they’re on their period. Having that understanding in a group, even as a joke, makes it easier to endure.
Menstruators’ pain is often brushed off and seen as something commonplace or routine - but a synced cycle means that at least one other person has it as bad as you - and probably gets what you’re going through.
Researcher Breanne Fahs also mentions that the kind of ‘don’t mess with us’ solidarity that syncing periods leads to - is actually kind of empowering. Menstruators can often be ridiculed for their anger, and their ‘hormonal moods’ are used against them to make them look ‘irrational’ and ‘emotional.’ These instances of group, or friend solidarity help them feel validated.
Basically, syncing up is bound to happen once in a while - but I see it as a fun reminder to go easy on each other, instead of a ~mystical~ ‘It’s A Match!’ from the period gods. Sorry that it’s not the witchy reasoning you would’ve liked, but honestly, if someone at home took the last Meftalspaz, you might still find your way around a curse.