The right hand figure isn't meant really to be measured.
I interpret it as, play that short note as short as you can while still having it be heard as a distinct note.
Yeah, I think that gets to the crux of the problem for me. If I'm aligning it to the LH note then it gets very tied into the arithmetic of it. If I play it slightly after the LH note, then it gets decoupled from the arithmetic in a way that feels a lot more comfortable. At speed that all sort of gets lost, but when working on the passage slowly I've had this weird discomfort with the idea that I might not be playing it properly.
Because the music is not aligned visually in the sheet music, it didn't really occur to me that they lined up until I decided to work out exactly how the polyrhythms relate and realised to my astonishment that they fall in the same place. Probably because I'd been playing it the other way so long, it felt unnatural and uncomfortable to line them up. And likely I play the semiquaver too short in the other sections by habit anyways when there's nothing to line it up to (like running semiquavers).
That said, there are so far three votes in favour of lining it up and one against, so I will definitely make the effort to see how it feels when they align after practicing it that way for a few days, and maybe that will get me to rethink slightly the other occurrences of the melody.