So after some fiddling around, I’ve figured out that passengers can be loaded correctly (but only in a subset of planes) by using the “quick fill” slider and then clicking “load in aircraft”. The issue remains where trying to do this manually (or should I say, not so quickly) by clicking on seats and entering weights does not have the desired effect.
It’s entirely possible that this is somewhere between a bug per se and just really counterintuitive UX; “quick” fill does imply that using that slider is optional.