No argument about lots of rivers having (or having had) rapids, as you describe! As far as watershed size goes, that is an interesting factor, but does it in fact help predict (in the real world) whether a given river has rapids/waterfalls/non-navigable parts? Is considering it actually useful for this purpose?
I'm really struck by the (apparent?) discontinuity between the Mssuma's relatively short length compared to the three big rivers you compare its catchment area to. Just doing an eyeball survey of Wikipedia, of the 23 rivers falling between 2000-2500km in length, only one has a drainage basin over a million square kilometers (the Orinoco, at just 1.3mkm2). To me that suggests the Mssuma you've laid out is a real outlier compared to its Earthly peers. And it also suggests to me that I should actually go look at one of the maps and see how long the Mssuma is, instead of going off old & ingrained memories that could be total BS.
Could the sheer
blankness of published maps of Tekumel be a factor? In my own experience doing this sort of thing (much less rigorously than you are, though!) once you start "filling in the blanks" on any one given project you have, there's an automatic creep of scale that happens. Or, I wonder, that alleged tendency is just how I justify my habit of starting at the peripheries and gradually working around & inward...

As a complete rube in these matters, my gut instinct would be: if the drainage area is large (relative to length), I imagine a flat and gentle topography~geology in the river basin, and hence
less likelihood of rapids etc. Not that I ever actually
have thought about this... until now

I'm not on Facebook, so I haven't seen the Bey Sü map you mention. Any scraps of information are valuable, and hard not to defer to -- but I guess my rule of thumb would be, any map that's "sketch" shouldn't be relied on for anything but relative orientation, size, and direction, and
especially discounted when it comes to any bodies of water
In any case, I haven't read your Digitizing Tekumel posts for years (I think that shows?) and I'm going to remedy that real soon -- and definitely before I bloviate any more here!