Stream-of-image video data and cinelerra
Just so I won't forget, but also to make sure others with similar problems to me don't need to search for several hours before finding it's so simple that it's silly:
If you have a bunch of image files (PNG, JPG, whatnot) that you want to treat as a single clip in cinelerra rather than hundreds (if not thousands) of individual files, the trick is to use a "list file": you create a file with some metadata and a list of all the files that make up the video clip, and import that, rather than the individual files.
If said individual files are PNG files with alpha information, doing so also makes it ridiculously easy to create an animation that only covers part of the screen.
The file format is pretty basic; but over at this page on the cinelerra.org website they list two scripts (one python with GUI, one bash and command-line only) that can generate such a file, given a bunch of image files. That makes it even easier.
I'd also like to note, for the record, that cinelerra outperforms kdenlive in everything but 'transcoding flexibility'. Kdenlive also has support for image lists (and you can create them in the gui rather than having to muck about with external programs or editors), but it has the rather nasty misfeature of doing the equivalent of "Oh, look, what's that? We don't need that, let's throw it away" whenever it encounters alpha information in PNG files.
For full reproducability, it's also possible to generate PNG files with alpha information from povray if you use the +UA command-line parameter, and say something like
sky_sphere { pigment { color rgbt <0, 0, 0, 1> } }
somewhere in your scene file. Yes, I know, povray is non-free, but it works, and—as opposed to blender—I do know how to use it. Hey, I'm not RMS.